From a3a02137024cd2b27e3b459850b4398b2b7cec8a Mon Sep 17 00:00:00 2001 From: glucksfall Date: Fri, 15 Mar 2019 12:24:07 -0300 Subject: [PATCH 01/17] Changes in CHANGES.md --- ...ptools API - Operations on Compounds.ipynb | 362 + ... - Operations on Enzymatic-Reactions.ipynb | 34762 ++++ .../ptools API - Operations on Genes.ipynb | 775 + .../ptools API - Operations on Pathways.ipynb | 11390 ++ ...ns on Proteins and Protein Complexes.ipynb | 1277 + ...ptools API - Operations on Reactions.ipynb | 122770 +++++++++++++++ ...PI - Operations on Regulation Frames.ipynb | 1411 + .../ptools API - enumeration operations.ipynb | 926 + pythoncyc/PGDB.py | 6790 +- pythoncyc/PTools.py | 320 +- pythoncyc/PToolsFrame.py | 457 +- pythoncyc/__init__.py | 19 +- pythoncyc/config.py | 59 +- setup.py | 36 +- 14 files changed, 177619 insertions(+), 3735 deletions(-) create mode 100644 examples/ptools API - Operations on Compounds.ipynb create mode 100644 examples/ptools API - Operations on Enzymatic-Reactions.ipynb create mode 100644 examples/ptools API - Operations on Genes.ipynb create mode 100644 examples/ptools API - Operations on Pathways.ipynb create mode 100644 examples/ptools API - Operations on Proteins and Protein Complexes.ipynb create mode 100644 examples/ptools API - Operations on Reactions.ipynb create mode 100644 examples/ptools API - Operations on Regulation Frames.ipynb create mode 100644 examples/ptools API - enumeration operations.ipynb diff --git a/examples/ptools API - Operations on Compounds.ipynb b/examples/ptools API - Operations on Compounds.ipynb new file mode 100644 index 0000000..1291a63 --- /dev/null +++ b/examples/ptools API - Operations on Compounds.ipynb @@ -0,0 +1,362 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", + "[u'|META|', u'|ECOLI|']\n", + "class-name-p\n", + "(class-name-p \"compounds\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"compounds\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Compounds| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Compounds| ))\n", + "get-class\n", + "(get-class |Compounds| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Compounds| ))\n", + "class-name-p\n", + "(class-name-p \"reactions\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"reactions\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Reactions| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Reactions| ))\n", + "get-class\n", + "(get-class |Reactions| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Reactions| ))\n", + "all-enzymes\n", + "(all-enzymes :type :chemical-change)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :chemical-change))\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "\n", + "compounds = [x.frameid for x in ecoli.compounds.instances][0:2]\n", + "reactions = [x.frameid for x in ecoli.reactions.instances][0:2]\n", + "enzymes = ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reactions-of-compound\n", + "(reactions-of-compound '|CPD0-1107| :enzymatic? t)\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-compound '|CPD0-1107| :enzymatic? t))\n", + "reactions-of-compound\n", + "(reactions-of-compound '|CPD-8521| :enzymatic? t)\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-compound '|CPD-8521| :enzymatic? t))\n", + "[[u'|RXN0-5298|'], [u'|RXN0-1922|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "cpd\n", + "A child of class |Compounds|. \n", + "non-specific-too?\n", + "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", + "parent of cpd, appears as a substrate. \n", + "transport-only?\n", + "Keyword, Optional If non-nil, return only transport reactions. \n", + "compartment\n", + "Keyword, Optional If non-nil, return only reactions within the specified \n", + "compartment. \n", + "enzymatic?\n", + "Keyword, Optional If non-nil, return only enzymatic reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.reactions_of_compound(compound, enzymatic = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "substrate-of-generic-rxn?\n", + "(substrate-of-generic-rxn? '|CPD0-1107| '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrate-of-generic-rxn? '|CPD0-1107| '|DSBD-RXN| ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for compound in compounds:\n", + " for reaction in reactions:\n", + " lst.append(ecoli.substrate_of_generic_rxn(compound, reaction))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pathways-of-compound\n", + "(pathways-of-compound '|CPD0-1107| )\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-compound '|CPD0-1107| ))\n", + "pathways-of-compound\n", + "(pathways-of-compound '|CPD-8521| )\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-compound '|CPD-8521| ))\n", + "[[u'|FUCCAT-PWY|', u'|FUC-RHAMCAT-PWY|'], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "cpd\n", + "An instance of class |Compounds|. \n", + "non-specific-too?\n", + "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", + "parent of cpd, appears as a substrate. \n", + "modulators?\n", + "Keyword, Optional If non-nil, returns pathways where cpd appears as a regulator \n", + "as well. \n", + "phys-relevant?\n", + "Keyword, Optional If true, then only return inhibitors that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "include-rxns?\n", + "Keyword, Optional If non-nil, then return a list of reaction-pathway pairs. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.pathways_of_compound(compound))#, modulators = True, include_rxns = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ACTIVATED-OR-INHIBITED-BY-COMPOUND\n", + "(ACTIVATED-OR-INHIBITED-BY-COMPOUND '|CPD0-1107| )\n", + "(with-organism (:org-id '|ECOLI|) (ACTIVATED-OR-INHIBITED-BY-COMPOUND '|CPD0-1107| ))\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "cpds\n", + "An instance or list of instances of class |Compounds|. \n", + "mode\n", + "Keyword, Optional Represents the type of regulation. Can take on the values of \n", + "“+”, “-”, or 'nil. \n", + "mechanisms\n", + "Keyword, Optional Keywords from the 'mechanism slot of the corresponding \n", + "sub-class of the class |Regulation|. If non-nil, only regulation objects with \n", + "mechanisms in this list will be explored for regulated objects. \n", + "phys-relevant?\n", + "Keyword, Optional If true, then only return inhibitors that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "slots\n", + "Keyword A list of enzymatic reaction slots to \n", + "\"\"\"\n", + "\n", + "try:\n", + " lst = []\n", + " for compound in compounds:\n", + " lst.append(ecoli.activated_or_inhibited_by_compound(compound))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "tfs-bound-to-compound\n", + "(tfs-bound-to-compound '|CPD0-1107| :include-inactive? t)\n", + "(with-organism (:org-id '|ECOLI|) (tfs-bound-to-compound '|CPD0-1107| :include-inactive? t))\n", + "tfs-bound-to-compound\n", + "(tfs-bound-to-compound '|CPD-8521| :include-inactive? t)\n", + "(with-organism (:org-id '|ECOLI|) (tfs-bound-to-compound '|CPD-8521| :include-inactive? t))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.tfs_bound_to_compound(compound, include_inactive = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": { + "scrolled": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "full-enzyme-name\n", + "(full-enzyme-name '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (full-enzyme-name '|DSBD-RXN| ))\n", + "full-enzyme-name\n", + "(full-enzyme-name '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (full-enzyme-name '|RXN0-4342| ))\n", + "[u'dsbd-rxn', u'rxn0-4342']\n", + "\n", + "enzyme-activity-name\n", + "(enzyme-activity-name '|MHPELY-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-activity-name '|MHPELY-MONOMER| nil ))\n", + "enzyme-activity-name\n", + "(enzyme-activity-name '|G6571-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-activity-name '|G6571-MONOMER| nil ))\n", + "[u'4-hydroxy-2-oxovalerate aldolase', u'L,D-transpeptidase YcfS']\n" + ] + } + ], + "source": [ + "# Object Name Manipulation Operations\n", + "# lst = []\n", + "# for reaction in reactions:\n", + "# lst.append(ecoli.get_name_string(reaction))\n", + "# print lst[-10:]\n", + "# print ''\n", + "\n", + "lst = []\n", + "for reaction in reactions:\n", + " lst.append(ecoli.full_enzyme_name(reaction))\n", + "print lst[-10:]\n", + "print ''\n", + "\n", + "lst = []\n", + "for enzyme in enzymes:\n", + " lst.append(ecoli.enzyme_activity_name(enzyme))\n", + "print lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Enzymatic-Reactions.ipynb b/examples/ptools API - Operations on Enzymatic-Reactions.ipynb new file mode 100644 index 0000000..e011b10 --- /dev/null +++ b/examples/ptools API - Operations on Enzymatic-Reactions.ipynb @@ -0,0 +1,34762 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", + "[u'|META|', u'|ECOLI|']\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns :all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns :all ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15348| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LACTALDREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PFLDEACTIV-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHMETPYRKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7094| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7298| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1137| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BADH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMKCYT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5061| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FES-OX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16000| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6505| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPCARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2601| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MENCYT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7003| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARNDETRU-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14505| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5118| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTAPD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16650| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEPHOSICITDEHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXNMETA-12672| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROTEIN-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTEIN-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5183| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5183| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYL-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10658| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16910| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12473| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12473| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2942| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2942| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|YIAE2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|YIAE2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17355| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17355| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|D-PPENTOMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|D-PPENTOMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14570| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14570| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19340| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19340| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5216| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5216| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5741| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5741| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17393| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17393| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METBALT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METBALT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9533| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9533| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROLINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROLINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9660| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9660| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYADENPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYADENPHOSPHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SPONTPRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SPONTPRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1144| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1144| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5292| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5292| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5098| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5098| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17701| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17701| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6435| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6435| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRIDOXINE-4-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIDOXINE-4-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6547| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6547| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIAMACTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMACTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3241| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3241| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-745| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-745| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5387| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5387| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17783| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17783| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14883| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14883| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.3.1.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.3.1.9-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R170-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R170-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.3.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.3.9-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGNAD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGNAD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|N-ACETYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|N-ACETYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARCB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5435| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5435| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBTSRD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTSRD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17799| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17799| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TAGAKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TAGAKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADPH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOSYLHOMOCYSTEINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOSYLHOMOCYSTEINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARLX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARLX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DUTP-PYROP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DUTP-PYROP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMINOBUTDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINOBUTDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRUFLAVREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUFLAVREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16330| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16330| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6359| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6359| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5245| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5245| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17935| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17935| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-385| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-385| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14107| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14107| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6490| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6490| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10851| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10851| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17014| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17014| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10981| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10981| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15140| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15140| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17474| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17474| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5254| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5254| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FMNREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FMNREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19445| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19445| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6954| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6954| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6462| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6462| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NICOTINAMID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICOTINAMID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8629| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8629| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17757| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17757| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.127-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.127-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9537| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9537| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5259| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5259| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18435| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18435| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THRESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THRESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9663| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9663| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-237| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-237| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11576| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11576| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18581| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18581| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTONOLACTONASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTONOLACTONASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARYLAMINE-N-ACETYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARYLAMINE-N-ACETYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5204| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5204| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5263| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5263| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6512| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6512| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6705| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6705| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MVHMETH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MVHMETH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1PFRUCTPHOSN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1PFRUCTPHOSN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7195| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19616| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19616| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19022| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19022| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-748| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-748| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16329| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16329| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11638| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11638| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15356| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15356| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UHPB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UHPB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5244| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5244| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUC1PADENYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUC1PADENYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.8.1.4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.1.4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17651| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17651| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6549| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6549| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ORNCARBAMTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ORNCARBAMTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-HYDROXYDECANOYL-ACP-DEHYDR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-HYDROXYDECANOYL-ACP-DEHYDR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5253| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5253| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.157-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.157-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHERTARM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHERTARM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6684| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6684| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19472| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19472| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRIPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRIPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|EVGA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|EVGA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17751| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17751| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11845| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11845| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYDH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5257| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5257| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAMINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BAES-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BAES-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NITRATE-REDUCTASE-CYTOCHROME-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NITRATE-REDUCTASE-CYTOCHROME-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-234| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-234| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6720| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6720| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-DIP-REDUCTI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-DIP-REDUCTI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17759| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17759| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.9.3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.9.3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16002| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16002| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11476| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11476| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5262| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5262| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19924| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19924| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14498| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14498| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19019| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19019| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12198| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12198| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEPCARBOXYKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPCARBOXYKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17017| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17017| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15815| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15815| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCEROL-2-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCEROL-2-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9514| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9514| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5242| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5242| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6952| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6952| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9550| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9550| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6372| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6372| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.11.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.11.2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9789| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9789| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16333| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16333| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5822| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5822| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CATAL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CATAL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2145| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2145| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5248| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5248| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12618| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12618| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5401| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5401| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6678| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6678| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYRIBONUCSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYRIBONUCSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5120| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5120| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7198| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7198| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17662| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17662| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6988| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6988| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-947| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-947| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5255| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5255| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.27.6-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.27.6-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16659| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16659| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.8.4.14-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.14-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7005| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7005| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7913| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7913| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-SYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-SYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17758| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17758| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13072| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13072| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHENYLALANINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENYLALANINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.11.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANOSINE-DIPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANOSINE-DIPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BASR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BASR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18603| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18603| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7021| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7021| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URIDINEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URIDINEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FERREDOXIN--NAD+-REDUCTASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FERREDOXIN--NAD+-REDUCTASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5265| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5265| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.13.22-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.22-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALONYL-ACPDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALONYL-ACPDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12827| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12827| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8642| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8642| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CPM-KDOSYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CPM-KDOSYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NRIPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NRIPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-924| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-924| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13990| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13990| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RSTA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RSTA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-283| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-283| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTIDINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTIDINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5184| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5184| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11479| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11479| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5252| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5252| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7080| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7080| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15510| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15510| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5456| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5456| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.5.1.88-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.5.1.88-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16937| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16937| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17020| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17020| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6489| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6489| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9560| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9560| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17897| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17897| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7288| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7288| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14116| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14116| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PMPOXI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PMPOXI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19619| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19619| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R148-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R148-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|IMP-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IMP-DEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9520| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9520| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-285| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-285| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7143| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7143| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DADPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DADPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9557| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9557| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4322| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4322| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.1.3.20-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.1.3.20-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1132| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1132| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5344| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5344| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1441| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1441| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5217| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5217| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5513| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5513| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5464| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5464| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7039| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7039| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6723| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6723| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17472| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17472| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-724| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-724| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R185-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R185-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7238| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7238| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-288| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-288| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOACETATE-DECARBOXYLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOACETATE-DECARBOXYLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROPIONATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROPIONATE--COA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.1.1.63-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.63-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2042| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2042| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.2.1.61-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.1.61-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5354| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5354| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14408| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14408| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYGLUCONOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYGLUCONOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BIOTINLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BIOTINLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LCYSDESULF-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LCYSDESULF-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CITTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7309| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7309| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5294| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5294| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FMN-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FMN-RED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R134-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R134-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACONITATEHYDR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATEHYDR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MCPTAP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTAP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2605| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2605| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17724| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17724| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOBR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOBR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-293| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-293| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14510| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14510| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10654| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10654| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4741| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4741| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-NADP+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-NADP+-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRIDOXKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIDOXKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11482| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11482| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|S-FORMYLGLUTATHIONE-HYDROLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|S-FORMYLGLUTATHIONE-HYDROLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17023| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17023| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6434| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6434| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENYLOSUCCINATE-SYNTHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLOSUCCINATE-SYNTHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18584| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18584| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7159| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7159| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2945| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2945| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19949| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19949| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R138-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R138-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14712| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14712| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5390| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5390| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9527| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9527| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2701| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2701| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHGLYSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHGLYSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9655| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9655| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-296| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-296| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCCOASYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCCOASYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17784| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17784| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1138| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1138| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5238| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5238| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALDEHYDE-DEHYDROGENASE-NADP+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALDEHYDE-DEHYDROGENASE-NADP+-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-321| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-321| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5392| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5392| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R303-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R303-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7095| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7095| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6467| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6467| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14968| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14968| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7297| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7297| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7172| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7172| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAD-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAD-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DMBPPRIBOSYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMBPPRIBOSYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TORT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TORT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R143-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R143-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TDPFUCACTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TDPFUCACTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.180-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.180-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMINOPROPDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINOPROPDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5437| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5437| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACYLGPEACYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLGPEACYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3021| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3021| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3921| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3921| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBDEP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBDEP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5251| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5251| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15210| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15210| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17809| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17809| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTD-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTD-RED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5454| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5454| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NMNAMIDOHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NMNAMIDOHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GCVT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GCVT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6471| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6471| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THYKI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYKI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOSYLNICOTINAMIDE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOSYLNICOTINAMIDE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MCPTSR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTSR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7287| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7287| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASNSYNA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASNSYNA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-A-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-A-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2841| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2841| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4581| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4581| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DXPREDISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DXPREDISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10657| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10657| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4161| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4161| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15513| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15513| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15915| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15915| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5332| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5332| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OROPRIBTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OROPRIBTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6366| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6366| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17354| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17354| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5463| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5463| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-GUANINE-N7--METHYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-GUANINE-N7--METHYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18678| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18678| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6707| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6707| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BASS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BASS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17936| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17936| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-20000| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-20000| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R167-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R167-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16009| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16009| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9532| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9532| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-287| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-287| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEPSYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPSYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11109| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11109| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9659| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9659| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4462| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4462| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPGLCNACEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPGLCNACEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5347| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5347| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CDPDIGLYSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPDIGLYSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FOLYLPOLYGLUTAMATESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FOLYLPOLYGLUTAMATESYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5055| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5055| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5487| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5487| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5122| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5122| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6546| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6546| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6989| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6989| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16664| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16664| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6478| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6478| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7108| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7108| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R131-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R131-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHENYLSERINE-ALDOLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENYLSERINE-ALDOLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-618| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-618| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1641| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1641| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UROGENDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UROGENDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.168-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.168-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-291| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-291| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CREC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CREC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.13.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.13.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4721| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4721| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5186| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5186| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18549| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18549| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARCA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5372| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5372| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16992| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16992| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBTRGD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTRGD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6409| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6409| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PNP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11578| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11578| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7071| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7071| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DALADALALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DALADALALIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GSADENYLATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSADENYLATION-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R137-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R137-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5222| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5222| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTURIDYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTURIDYLYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARLQ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARLQ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-269| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-269| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17489| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17489| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYFLAVOXRE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYFLAVOXRE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-295| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-295| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6515| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6515| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10660| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10660| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5230| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5230| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYINOPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYINOPHOSPHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13039| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13039| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5389| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5389| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5297| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5297| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1TRANSKETO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1TRANSKETO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17013| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17013| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6466| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6466| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17726| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17726| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17363| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17363| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7171| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7171| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRIMSYN3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIMSYN3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19024| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19024| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19366| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19366| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R140-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R140-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIAMTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7716| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7716| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-278| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-278| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5393| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5393| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11776| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11776| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9536| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9536| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17786| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17786| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9662| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9662| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5250| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5250| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R524-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R524-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUC1PURIDYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUC1PURIDYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-20| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-20| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5450| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5450| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DNA-CYTOSINE-5--METHYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-CYTOSINE-5--METHYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5194| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5194| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6470| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6470| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6550| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6550| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6445| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6445| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7279| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7279| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17847| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17847| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6561| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6561| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-284| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-284| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBULP3EPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBULP3EPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.4.1.230-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.4.1.230-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7192| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7192| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-DELTA-ISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-DELTA-ISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-747| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-747| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5307| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5307| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6368| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6368| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19474| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19474| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5459| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5459| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17954| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17954| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.7.2.3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.7.2.3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6571| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6571| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17960| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17960| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11860| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11860| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2OXOGLUTDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2OXOGLUTDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-921| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-921| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11152| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11152| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BAER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BAER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R166-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R166-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FORMYLTHFGLUSYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FORMYLTHFGLUSYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAMINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMINESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHERTAPM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHERTAPM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-286| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-286| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6480| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6480| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENVZ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENVZ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-443| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-443| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.251-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.251-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6721| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6721| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYDG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5345| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5345| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18586| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18586| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARPX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARPX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5465| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5465| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11588| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11588| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.8.1.6-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.8.1.6-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|REDUCEDFE-S-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|REDUCEDFE-S-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6949| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6949| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALPMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALPMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11474| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11474| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5077| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5077| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6521| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6521| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19953| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19953| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14391| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14391| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-290| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-290| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-ISOPROPYLMALATESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-ISOPROPYLMALATESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17016| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17016| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19026| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19026| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12274| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12274| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17824| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17824| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5358| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5358| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11811| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11811| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19473| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19473| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6362| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6362| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCEROL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCEROL-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8668| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8668| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7069| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7069| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6556| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9540| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9540| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R136-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R136-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.5.1.19-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.5.1.19-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6957| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6957| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9788| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9788| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-266| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-266| ))\n", + 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)\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.13-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-298| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-298| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6974| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6974| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-SYNTH-BASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-SYNTH-BASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5239| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5239| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.13.3-RXN| )\n", + "(with-organism (:org-id 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"cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6468| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6468| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12754| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12754| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.3.68-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.3.68-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FAD-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FAD-RED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7266| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7266| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GMP-SYN-GLUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GMP-SYN-GLUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NRIIPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NRIIPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7294| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7294| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6994| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6994| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7931| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7931| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-TRIP-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-TRIP-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.1.14-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.1.14-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11478| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11478| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CPXR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CPXR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7967| )\n", + 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))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANYL-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANOSINEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANOSINEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19618| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19618| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URIDYLREM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URIDYLREM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7024| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7024| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9518| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9518| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6519| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6519| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.17.8-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.17.8-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7022| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7022| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9556| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9556| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7284| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7284| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8667| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8667| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-982| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-982| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14023| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14023| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.13.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.9-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2721| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2721| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTPRATPHYD-RXN| )\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTPRATPHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5468| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5468| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7090| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7090| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8645| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8645| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6499| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6499| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|325-BISPHOSPHATE-NUCLEOTIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|325-BISPHOSPHATE-NUCLEOTIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-723| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-723| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9772| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9772| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14002| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14002| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TDCEACT1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TDCEACT1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14136| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14136| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.97.1.4-A-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.97.1.4-A-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|INORGPYROPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INORGPYROPHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTIDPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTIDPHOS-RXN| ))\n", + 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)\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FMN-OX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDPGALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDPGALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MCPMETEST-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPMETEST-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7249| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7249| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9562| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9562| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOBCREC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOBCREC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOLACTREDUCTOISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOLACTREDUCTOISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10462| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10462| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-21| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-21| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14124| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14124| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14473| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14473| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15512| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15512| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LIPIDADISACCHARIDESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LIPIDADISACCHARIDESYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|IMPCYCLOHYDROLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IMPCYCLOHYDROLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17022| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17022| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-884| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-884| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18434| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18434| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACYLCOADEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLCOADEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7154| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7154| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19780| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19780| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2621| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2621| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9524| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9524| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14513| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14513| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.3.1.17-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.3.1.17-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9590| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9590| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALTACETYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALTACETYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1134| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1134| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SEDOBISALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SEDOBISALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-312| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-312| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADPSUGPPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADPSUGPPHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-301| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-301| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6507| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6507| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14806| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14806| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7084| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7084| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHYLENETHFDEHYDROG-NADP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLENETHFDEHYDROG-NADP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDOTRANS2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDOTRANS2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7271| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7271| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCGLUDESUCC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCGLUDESUCC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALKAPHOSPHA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALKAPHOSPHA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7239| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7239| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.179-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.179-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACP-S-ACETYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACP-S-ACETYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15041| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15041| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOACETYL-COA-TRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOACETYL-COA-TRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBDEAMID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBDEAMID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROGENASE-QUINONE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROGENASE-QUINONE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYT-ACC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYT-ACC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THI-P-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THI-P-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2044| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2044| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GCVP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GCVP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MCPTRG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTRG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3962| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3962| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14409| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14409| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSICITDEHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15293| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15293| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10656| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10656| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIP-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIP-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LEUCINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LEUCINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15891| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15891| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THYMIDYLATESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYMIDYLATESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17127| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17127| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARAGINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARAGINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-742| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-742| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18605| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18605| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4841| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4841| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19952| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19952| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15607| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15607| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACSERLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACSERLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9531| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9531| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OXALODECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALODECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9658| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9658| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-S-TRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-S-TRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2606| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2606| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1140| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1140| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BETA-PHOSPHOGLUCOMUTASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETA-PHOSPHOGLUCOMUTASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4942| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4942| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5065| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5065| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14511| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14511| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6385| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6385| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-1623| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-1623| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6533| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6533| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGLUCISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLUCISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALIC-NADP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALIC-NADP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7105| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7105| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPMANACATRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPMANACATRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7303| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7303| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SAICARSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SAICARSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-583| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-583| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5125| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5125| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.49-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.49-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16687| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16687| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENYLYLSULFKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLYLSULFKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALTARCA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTARCA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSACETYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSACETYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEBTARD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTARD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-299| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-299| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DISULFOXRED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DISULFOXRED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYCPHOSDIESTER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYCPHOSDIESTER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAREDOXIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAREDOXIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5190| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5190| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14747| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14747| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MYRPALMTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MYRPALMTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16997| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16997| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROTEIN-TYROSINE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTEIN-TYROSINE-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|POLYPHOSPHATE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|POLYPHOSPHATE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHIONINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHIONINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10659| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10659| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DARABALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17012| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17012| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5225| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5225| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCDIAMINOPIMDESUCC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCDIAMINOPIMDESUCC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17362| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17362| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17495| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17495| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19342| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19342| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRPPAMIDOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRPPAMIDOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALDOSE-1-EPIMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALDOSE-1-EPIMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYRIBOSE-P-ALD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYRIBOSE-P-ALD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9535| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9535| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5305| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5305| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3364| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3364| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17753| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17753| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1147| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1147| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14992| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14992| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5177| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5177| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDRODIPICSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDRODIPICSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6442| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6442| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5402| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5402| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-GLN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-GLN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6560| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6560| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17789| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17789| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7169| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7169| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RHAMNISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RHAMNISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TETHYDPICSUCC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TETHYDPICSUCC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-746| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-746| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DNA-LIGASE-NAD+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-LIGASE-NAD+-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMACYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMACYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5509| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5509| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMP-DEPHOSPHORYLATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMP-DEPHOSPHORYLATION-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.7.2.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.7.2.2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17887| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17887| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.7.61-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.61-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RNTRACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RNTRACTIV-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3922| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3922| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ATOC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATOC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENTF-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTF-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15216| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15216| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOLO-ACP-SYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOLO-ACP-SYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18031| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18031| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARPQ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARPQ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11319| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11319| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NMNNUCLEOSID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NMNNUCLEOSID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RCSC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RCSC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FUC4NACTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUC4NACTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6483| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6483| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THYM-PHOSPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYM-PHOSPH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.274-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.274-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17015| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17015| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18707| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18707| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPAMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPAMINOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17823| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17823| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11592| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11592| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8655| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8655| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GARTRANSFORMYL2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GARTRANSFORMYL2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4621| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4621| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9539| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9539| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6524| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6524| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9787| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9787| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15578| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15578| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2142| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2142| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19256| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19256| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5211| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5211| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11834| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11834| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OROTPDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OROTPDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7196| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7196| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCONOLACT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCONOLACT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-801| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-801| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6564| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6564| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-NUCLEOTIDYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-NUCLEOTIDYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UHPC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UHPC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.6.1.7-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.6.1.7-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.8.4.12-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.12-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19737| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19737| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BETA-GLUCURONID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETA-GLUCURONID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-OXOACYL-ACP-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12070| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12070| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHERTRGM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHERTRGM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5062| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5062| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FAD-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FAD-OX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6731| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6731| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LAUROYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LAUROYLACYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16165| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16165| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NRIDEPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NRIDEPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-2425| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2425| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-DIP-REDUCTII-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBONUCLEOSIDE-DIP-REDUCTII-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12445| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12445| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEPTIDYLPROLYL-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPTIDYLPROLYL-ISOMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11477| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11477| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCOLALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLALDREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14499| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14499| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6977| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6977| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPGLUCEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPGLUCEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17018| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17018| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.21.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19617| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19617| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-6423| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6423| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9516| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9516| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12862| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12862| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9555| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9555| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GPPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GPPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5123| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5123| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9790| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9790| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7000| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7000| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-267| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-267| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.1.52-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.1.52-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16665| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16665| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5419| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5419| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8315| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8315| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6495| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6495| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13329| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13329| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOQ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOQ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-722| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-722| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-949| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-949| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7040| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7040| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UROGENIIISYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UROGENIIISYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.8.4.8-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.8-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.105-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.105-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.3.16-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.3.16-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8899| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8899| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CROBETREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CROBETREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.2.1.58-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.1.58-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14047| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14047| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CITC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5187| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5187| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FLAVONADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FLAVONADPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALONYL-COA-ACP-TRANSACYL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALONYL-COA-ACP-TRANSACYL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4-NITROPHENYLPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4-NITROPHENYLPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16995| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16995| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PALMITOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PALMITOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9983| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9983| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RSTB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RSTB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14143| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14143| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PNPOXI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNPOXI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11480| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11480| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|INOSINEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15511| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15511| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7168| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7168| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DAPASYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DAPASYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17021| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17021| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.99.1.3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.99.1.3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17943| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17943| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1842| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1842| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5223| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5223| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19774| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19774| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14286| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14286| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9523| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9523| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KETOBUTFORMLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOBUTFORMLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17490| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17490| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9558| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9558| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7253| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7253| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1133| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1133| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROTOHEMEFERROCHELAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTOHEMEFERROCHELAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-307| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-307| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2201| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2201| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5514| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5514| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14479| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14479| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYNUCLEOTIDE-3-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYNUCLEOTIDE-3-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6503| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6503| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LTARTDEHYDRA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LTARTDEHYDRA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7047| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7047| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-962| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-962| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5298| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5298| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7268| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7268| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADCLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADCLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-REDUCT-NADPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-REDUCT-NADPH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-268| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-268| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17745| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17745| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.128-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.128-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14521| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14521| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-22-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-22-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNITOL-1-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNITOL-1-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRNUTRANSHYDROGEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRNUTRANSHYDROGEN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SERINE-O-ACETTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SERINE-O-ACETTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CREB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CREB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AICARTRANSFORM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AICARTRANSFORM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIENOYLCOAREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIENOYLCOAREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GAMMA-GLUTAMYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GAMMA-GLUTAMYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-304| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-304| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MCPTAR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTAR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14809| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14809| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5395| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5395| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10655| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10655| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-MUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-MUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11483| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11483| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCORNTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCORNTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17787| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17787| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15890| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15890| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALLOSE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLOSE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17024| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17024| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3543| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3543| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R621-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R621-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18604| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18604| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15122| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15122| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19950| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19950| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAG1P-URIDYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAG1P-URIDYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-DNA-POLYMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-DNA-POLYMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9528| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9528| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9657| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9657| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARABISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARABISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5462| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5462| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1139| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1139| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4181| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4181| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3341| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3341| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15298| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15298| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17848| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17848| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7299| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7299| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|O-SUCCHOMOSERLYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|O-SUCCHOMOSERLYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-582| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-582| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-623| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-623| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBULPEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBULPEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.41-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.41-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-549| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-549| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5021| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5021| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-HYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-HYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-569| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-569| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15761| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15761| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-588| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-588| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6371| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6371| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-609| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-609| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERILEU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERILEU-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17955| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17955| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-117| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-117| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5100| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5100| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-137| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-137| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16312| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16312| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17961| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17961| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-226| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-226| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLMURAMATEDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLMURAMATEDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11277| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11277| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5264| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5264| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHORISMATEMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORISMATEMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-273| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-273| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5129| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5129| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FPPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FPPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRUVDEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUVDEH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16690| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16690| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-295| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-295| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSNACMURPENTATRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSNACMURPENTATRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-328| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-328| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|VALINE-PYRUVATE-AMINOTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|VALINE-PYRUVATE-AMINOTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-35| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-35| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYSTEINE-AMINOTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTEINE-AMINOTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.264-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.264-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-366| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-366| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5199| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5199| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-58| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-58| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17009| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17009| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18702| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18702| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PPGPPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPGPPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12588| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12588| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DCDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11589| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11589| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-209| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-209| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5228| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5228| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12894| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12894| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17631| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17631| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GAPOXNPHOSPHN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GAPOXNPHOSPHN-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-258| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-258| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PSERTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PSERTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-280| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-280| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DGDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DGDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-452| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-452| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5329| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5329| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-473| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-473| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17776| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17776| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7204| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7204| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRUVFORMLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUVFORMLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1802| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1802| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19249| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19249| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-10-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-10-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5409| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5409| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7231| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7231| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17792| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17792| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11832| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11832| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-28-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-28-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIB5PISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIB5PISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-511| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-511| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTDPDEHYRHAMREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPDEHYRHAMREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCONATE-5-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCONATE-5-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-8-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-8-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6254| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6254| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-529| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-529| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17911| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17911| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6562| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6562| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-533| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-533| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10017| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10017| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-553| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-553| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ERYTHRON4PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ERYTHRON4PDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.5.1.64-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.5.1.64-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-572| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-572| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6418| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6418| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15315| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15315| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18093| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18093| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19629| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19629| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-591| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-591| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11397| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11397| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-612| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-612| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FUCULOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUCULOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11867| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11867| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6487| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6487| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.83-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.83-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18710| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18710| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-162| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-162| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11598| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11598| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6726| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6726| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-237| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-237| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5269| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5269| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6527| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6527| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2PGADEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2PGADEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-279| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-279| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYLPHENOL-HYDROX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYLPHENOL-HYDROX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-298| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-298| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19334| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19334| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROOROTATE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROOROTATE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19998| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19998| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11837| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11837| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-335| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-335| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOSE-1-PHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSE-1-PHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12402| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12402| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-352| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-352| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6575| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6575| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-369| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-369| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.10.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.10.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCOGENSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOGENSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19777| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19777| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-98| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn 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"cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6734| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6734| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.13.5-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.13.5-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-283| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-283| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-457| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-457| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-2962| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2962| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-6268| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6268| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1565| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1565| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12508| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12508| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-476| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-476| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCPDIESTER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCPDIESTER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12816| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12816| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7207| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7207| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6980| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6980| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-13-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-13-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.22.4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.22.4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GMP-SYN-NH3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GMP-SYN-NH3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-497| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-497| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7282| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7282| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7241| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7241| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12870| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12870| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6998| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6998| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-33-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-33-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GSPAMID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSPAMID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-514| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-514| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7007| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7007| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.1.17-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.1.17-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.2.23-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.2.23-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-536| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-536| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8344| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8344| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7968| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7968| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-558| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-558| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18092| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18092| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13460| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13460| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-575| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-575| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|H2PTEROATESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2PTEROATESYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13202| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13202| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4083| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4083| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11396| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11396| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7066| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7066| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROG-A-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROG-A-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.83-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.83-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANYLCYC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANYLCYC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-595| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-595| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FUCPALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUCPALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8992| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8992| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4701| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4701| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14073| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14073| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-703| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-703| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-616| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-616| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6485| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6485| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMSUCTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMSUCTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108D| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108D| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7104| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7104| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.19.12-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.19.12-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.39-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.39-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.2.99.18-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.99.18-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-144| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-144| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1241| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1241| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8675| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8675| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CITLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18709| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18709| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14181| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14181| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISOCHORSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCHORSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14025| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14025| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-241| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-241| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11596| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11596| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7187| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7187| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-282| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-282| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|6PGLUCONOLACT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6PGLUCONOLACT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSMET-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSMET-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-3| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-3| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDP-GLUCOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDP-GLUCOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1863| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1863| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-338| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-338| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7092| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7092| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-355| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-355| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6526| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6526| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|L-GLN-FRUCT-6-P-AMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-GLN-FRUCT-6-P-AMINOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-376| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-376| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7275| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7275| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3PGAREARR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3PGAREARR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-71| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-71| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETYLGLUTKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLGLUTKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-162| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-162| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9951| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9951| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-224| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-224| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19312| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19312| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14483| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14483| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13158| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13158| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LYSDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14139| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14139| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-269| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-269| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11836| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11836| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-985| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-985| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-288| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-288| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENODEAMIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENODEAMIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|INOSINATE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINATE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-0| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-0| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2787| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2787| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.6.3.23-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.23-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14524| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14524| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7166| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7166| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6566| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6566| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNONOXIDOREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNONOXIDOREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-480| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-480| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SIROHEME-FERROCHELAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SIROHEME-FERROCHELAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.4.2.10-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.4.2.10-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7210| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7210| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.1.148-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.1.148-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALADEHYDCHLORO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALADEHYDCHLORO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-16-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-16-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-310| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-310| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1603| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1603| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-500| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-500| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19776| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19776| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14812| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14812| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7244| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7244| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MHPELY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPELY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14284| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14284| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-36-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-36-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12072| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12072| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SULFATE-ADENYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFATE-ADENYLYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-518| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-518| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALTRO-OXIDOREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTRO-OXIDOREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDUD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDUD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2561| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2561| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTKIN-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-363| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-363| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-539| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-539| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15125| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15125| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7250| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7250| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-561| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-561| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6733| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6733| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NANK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NANK-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THREDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOLACTSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOLACTSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-578| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-578| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-SYNTHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-SYNTHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARGDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-600| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-600| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-1| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-1| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-2961| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2961| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15313| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15313| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108G| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108G| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14477| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14477| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12480| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12480| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRE6PHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRE6PHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5202| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5202| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LIPIDXSYNTHESIS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LIPIDXSYNTHESIS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-181A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-181A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCOPHOSPHORYL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOPHOSPHORYL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5040| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5040| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-25| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-25| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15889| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15889| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-901| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-901| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-285| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-285| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6979| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6979| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PANTEPADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTEPADENYLYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5388| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5388| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TYROSINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TYROSINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACYLCOASYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLCOASYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-31| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-31| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.21.7-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.7-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BTUR2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BTUR2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-341| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-341| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5107| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5107| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2625| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2625| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-359| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-359| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7253| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7253| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16456| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16456| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-379| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-379| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UNDECAPRENYL-DIPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UNDECAPRENYL-DIPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14514| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14514| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-77| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-77| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12869| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12869| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CITSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-201| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-201| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5144| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5144| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALTODEG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALTODEG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAMATESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMATESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GSDEADENYLATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSDEADENYLATION-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16765| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16765| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-228| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-228| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHASERSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHASERSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SELENOCYSTEINE-LYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SELENOCYSTEINE-LYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-273| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-273| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7002| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7002| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|XYLISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-444| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-444| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTIDEAM2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDEAM2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AGMATIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AGMATIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7124| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7124| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.2.21-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.2.21-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5209| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5209| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-11| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-11| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17307| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17307| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-302| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-302| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-464| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-464| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8342| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8342| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7190| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7190| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DCUS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCUS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14807| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14807| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1684| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1684| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13459| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13459| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5240| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5240| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-487| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-487| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17634| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17634| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHYLISOCITRATE-LYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLISOCITRATE-LYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7217| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7217| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|H2PTERIDINEPYROPHOSPHOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2PTERIDINEPYROPHOSPHOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PTAALT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PTAALT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DHBDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHBDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-503| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-503| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-705| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-705| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5363| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5363| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7247| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7247| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17779| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17779| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALLANTOATE-DEIMINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLANTOATE-DEIMINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-42-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-42-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.53-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.53-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|QUINOLINATE-SYNTHA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QUINOLINATE-SYNTHA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROXYISOVALDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROXYISOVALDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3521| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3521| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-544| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-544| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8991| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8991| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5414| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5414| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-564| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-564| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17795| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17795| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15119| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15119| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-584| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-584| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14065| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14065| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNDEAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNDEAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-604| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-604| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NADPH-DEHYDROGENASE-FLAVIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADPH-DEHYDROGENASE-FLAVIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMOSERKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOSERKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6271| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6271| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-112| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-112| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17919| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17919| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THI-P-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THI-P-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-129| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-129| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7103| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7103| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10639| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10639| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|F16ALDOLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|F16ALDOLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMYLOMALT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMYLOMALT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-205A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-205A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.2.1.99-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.1.99-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6446| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6446| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-262| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-262| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6452| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6452| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4022| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4022| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-290| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-290| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1081| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1081| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18258| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18258| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R601-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R601-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11475| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11475| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15296| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15296| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-313| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-313| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14161| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14161| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTARDEHYDRA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTARDEHYDRA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6502| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6502| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-346| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-346| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISOCHORMAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCHORMAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.2.99.7-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.2.99.7-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-362| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-362| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18739| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18739| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-42| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-42| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7173| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7173| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11602| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11602| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-82| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-82| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDPPYPHOSKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPPYPHOSKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARTASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-204| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-204| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|6PFRUCTPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6PFRUCTPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6531| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6531| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-236| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-236| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.1.1.72-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.72-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4961| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4961| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-276| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-276| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1862| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1862| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19343| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19343| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-447| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-447| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11840| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11840| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15743| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15743| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-467| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-467| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14325| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14325| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCUROISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCUROISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7200| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7200| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6677| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6677| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OXALYL-COA-DECARBOXYLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALYL-COA-DECARBOXYLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1702| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1702| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|L-ASPARTATE-OXID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-ASPARTATE-OXID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.7.13-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.13-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-492| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-492| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19919| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19919| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-URACIL-5--METHYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-URACIL-5--METHYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7222| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7222| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7272| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7272| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12107| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12107| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-24-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-24-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLY3KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLY3KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BETAGALACTOSID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETAGALACTOSID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-507| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-507| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETYLESTERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLESTERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6944| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6944| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-63-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-63-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-NUCLEOTID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5073| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5073| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-525| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-525| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2301| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2301| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-3523| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3523| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-547| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-547| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12541| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12541| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-568| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-568| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOXI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-587| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-587| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6983| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6983| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGLUCONDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLUCONDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-608| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-608| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LXULRU5P-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LXULRU5P-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.26.3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7609| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7609| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPMANNACADEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPMANNACADEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-116| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-116| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-984| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-984| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12876| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12876| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-132| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-132| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-I-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-I-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHEYDEPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEYDEPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENINE-DEAMINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENINE-DEAMINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7012| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7012| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-22| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-22| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.11.4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5126| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5126| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5260| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5260| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-275| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-275| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17755| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17755| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-1381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-1381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16688| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16688| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-272| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-272| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14523| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14523| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HEMN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HEMN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5309| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5309| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7074| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7074| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSGLYPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSGLYPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-294| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-294| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNONDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNONDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.92-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.92-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-325| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-325| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9087| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9087| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URUR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URUR-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-349| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-349| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14091| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14091| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11193| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11193| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYPOTAURINE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYPOTAURINE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYSTATHIONINE-BETA-LYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTATHIONINE-BETA-LYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-365| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-365| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AKBLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AKBLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7119| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7119| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6554| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6554| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4OHBENZOATE-OCTAPRENYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4OHBENZOATE-OCTAPRENYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5192| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5192| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-57| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-57| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-308| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-308| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1342| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1342| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-92| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-92| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14249| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14249| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16998| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16998| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-207| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-207| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14811| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14811| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISPH2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISPH2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12893| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12893| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7227| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7227| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PORPHOBILSYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PORPHOBILSYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-244| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-244| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MHPCHYDROL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPCHYDROL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACECOATRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACECOATRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7041| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7041| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1941| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1941| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DARABISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-279| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-279| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUGAR-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUGAR-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-451| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-451| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|L-RHAMNONATE-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-RHAMNONATE-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5226| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5226| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-470| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-470| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALPHAGALACTOSID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALPHAGALACTOSID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7285| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7285| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7203| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7203| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACID-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACID-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17629| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17629| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-18| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-18| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2441| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2441| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-27-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-27-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRPPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRPPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-510| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-510| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15124| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15124| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LYXISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYXISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2421| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2421| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN66-526| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN66-526| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEPHOSPHOCOAKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEPHOSPHOCOAKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-70-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-70-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NANE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NANE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENPHOSPHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-528| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-528| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2921| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2921| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5306| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5306| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-551| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-551| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIOSULFATE-SULFURTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOSULFATE-SULFURTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14552| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14552| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-571| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-571| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNPISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNPISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17754| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17754| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15314| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15314| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARCBTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCBTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SPERMACTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SPERMACTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-590| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-590| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALARACECAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALARACECAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4223| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4223| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3201| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3201| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-611| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-611| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14850| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14850| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATEREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATEREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15312| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15312| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUCOSAMINE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUCOSAMINE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASNSYNB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASNSYNB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUPEROX-DISMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUPEROX-DISMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5407| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5407| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMINEOXID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINEOXID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-383| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-383| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17790| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17790| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-161| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-161| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANSENOYLCOARED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANSENOYLCOARED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15131| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15131| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-236| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-236| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RHAMNULOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RHAMNULOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5268| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5268| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPCARBTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPCARBTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THREONINE-ALDOLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREONINE-ALDOLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-278| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-278| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARGSUCCINLYA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGSUCCINLYA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DSERDEAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSERDEAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-297| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-297| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5039| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5039| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4341| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4341| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-330| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-330| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15346| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15346| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5510| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5510| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-351| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-351| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15881| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15881| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OHMETHYLBILANESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHMETHYLBILANESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-368| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-368| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TREHALOSEPHOSPHA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALOSEPHOSPHA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17900| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17900| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PABASYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PABASYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ATPPHOSPHORIBOSYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPPHOSPHORIBOSYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.6.1.82-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.6.1.82-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5057| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5057| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10015| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10015| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TSA-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TSA-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15952| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15952| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-212| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-212| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PDXJ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PDXJ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENTMULTI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTMULTI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERVAL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERVAL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALA-GLU-LIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALA-GLU-LIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-265| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-265| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CARDIOLIPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARDIOLIPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6388| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6388| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7050| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7050| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5103| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5103| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5116| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5116| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-282| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-282| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16649| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16649| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18032| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18032| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-454| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-454| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16424| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16424| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHENDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-475| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-475| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UREIDOGLYCOLATE-LYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UREIDOGLYCOLATE-LYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11326| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11326| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7206| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7206| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGPPHOSPHA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGPPHOSPHA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|COBINAMIDEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBINAMIDEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-12-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-12-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5182| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5182| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FUCISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUCISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-496| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-496| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UGD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UGD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16909| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16909| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISOCITDEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCITDEH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLUCMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLUCMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6484| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6484| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-32-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-32-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CITRATE-PRO-3S-LYASE-THIOLESTERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITRATE-PRO-3S-LYASE-THIOLESTERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|YIAE1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|YIAE1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-513| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-513| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|D--TARTRATE-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|D--TARTRATE-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.283-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.283-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5214| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5214| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-532| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-532| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17392| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17392| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18708| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18708| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-535| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-535| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16701| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16701| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-557| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-557| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXPHOSGALACT-ALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXPHOSGALACT-ALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11593| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11593| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-574| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-574| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHASERDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHASERDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5291| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5291| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-593| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-593| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17700| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17700| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GCVMULTI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GCVMULTI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-615| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-615| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|XANTHOSINEPHOSPHORY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XANTHOSINEPHOSPHORY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRAZIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRAZIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108C| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108C| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIACYLGLYKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIACYLGLYKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6525| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6525| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTIDEAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDEAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5383| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5383| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-142| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-142| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17782| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17782| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-OHPHENOL-METHY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-OHPHENOL-METHY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5208| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5208| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R165-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R165-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17663| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17663| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIOHBUTANONEPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIOHBUTANONEPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19311| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19311| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-24| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-24| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17011| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17011| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5433| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5433| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17798| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17798| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11835| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11835| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRAISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRAISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOPHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-337| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-337| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DURIDKI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DURIDKI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-6-P-DEAMIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-6-P-DEAMIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6370| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6370| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DCTP-PYROPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCTP-PYROPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6277| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6277| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-354| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-354| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17931| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17931| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6565| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6565| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-372| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-372| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5234| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5234| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10819| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10819| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-69| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-69| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FCLEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FCLEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.1.121-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.1.121-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-0244| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-0244| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17633| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17633| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10940| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10940| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-222| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-222| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FHLMULTI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FHLMULTI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19775| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19775| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-268| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-268| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PSEUDOURIDINE-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PSEUDOURIDINE-KINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-286| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-286| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18392| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18392| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12071| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12071| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-460| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-460| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DHBAMPLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHBAMPLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11574| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11574| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7186| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7186| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTONDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTONDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-479| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-479| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6510| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6510| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7209| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7209| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.8.4.4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6732| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6732| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-15-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-15-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17778| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17778| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19004| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19004| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-499| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-499| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11637| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11637| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7243| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7243| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|QUERCETIN-23-DIOXYGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QUERCETIN-23-DIOXYGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLU6PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLU6PDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-22| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-22| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6542| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6542| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-2881| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2881| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-35-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-35-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.3.1.118-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.118-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-517| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-517| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19407| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19407| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12458| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12458| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2542| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2542| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5413| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5413| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11843| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11843| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-538| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-538| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAMIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCOLATEDEHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLATEDEHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-560| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-560| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17794| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17794| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6717| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6717| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-577| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-577| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.8.25-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.8.25-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6978| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6978| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-598| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-598| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19922| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19922| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-622| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-622| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12197| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12197| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.21.3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108F| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108F| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTDPGLUCOSEPP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPGLUCOSEPP-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCEROL-1-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCEROL-1-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6950| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6950| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-6622| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6622| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5130| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5130| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6259| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6259| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.11.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.11.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-146| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-146| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5647| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5647| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12864| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12864| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5201| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5201| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17918| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17918| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12611| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12611| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-169| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-169| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOXYLATE-REDUCTASE-NADP+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXYLATE-REDUCTASE-NADP+-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GSAAMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSAAMINOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10040| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10040| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6987| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6987| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-284| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-284| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.27.5-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.27.5-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-300| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-300| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|EXOPOLYPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|EXOPOLYPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7800| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7800| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-340| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-340| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12896| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12896| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.2.10-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.2.10-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6375| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6375| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6444| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6444| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANINE-DEAMINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANINE-DEAMINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-357| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-357| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7020| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7020| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8340| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6491| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6491| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6451| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6451| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.13.21-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.21-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-378| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-378| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8632| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8632| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13418| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13418| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19778| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19778| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18241| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18241| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13859| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13859| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-76| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-76| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTCYCLOHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTCYCLOHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|H2NTPEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2NTPEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-200| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-200| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11410| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11410| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7079| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7079| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-227| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-227| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.24.70-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.24.70-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7046| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7046| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13179| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13179| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GABATRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GABATRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9559| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9559| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-272| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-272| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14115| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14115| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.107-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.107-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7077| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7077| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6494| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6494| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|IMIDPHOSDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IMIDPHOSDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-418| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-418| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8974| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8974| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7123| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7123| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.13.11.16-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.13.11.16-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5-OXOPROLINASE-ATP-HYDROLYSING-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-OXOPROLINASE-ATP-HYDROLYSING-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.6.3.53-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.53-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1402| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1402| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14064| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14064| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-463| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-463| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18738| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18738| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14260| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14260| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7189| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7189| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDO-8PSYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDO-8PSYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMOSERDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOSERDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1682| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1682| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11601| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11601| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7235| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7235| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-486| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-486| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETATEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETATEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7102| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7102| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7215| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7215| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDPMANMANHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPMANMANHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2023| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2023| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1924| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1924| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14396| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14396| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.1.2.28-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.1.2.28-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-19-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-19-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6529| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6529| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LCARNCOALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LCARNCOALIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-502| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-502| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7304| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7304| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7246| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7246| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.1.1.34-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.34-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACONITATEDEHYDR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATEDEHYDR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2604| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2604| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14160| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14160| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-520| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-520| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19341| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19341| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14509| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14509| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-541| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-541| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-ACCEPTOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-ACCEPTOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|IPPISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IPPISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-563| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-563| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11839| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11839| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|S-ADENMETSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|S-ADENMETSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15294| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15294| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENYLATECYC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLATECYC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7170| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7170| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-580| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-580| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2943| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2943| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-603| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-603| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14693| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14693| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|6-PHOSPHO-BETA-GLUCOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6-PHOSPHO-BETA-GLUCOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-100| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-100| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6676| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6676| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHENYLTHFCYCLOHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHENYLTHFCYCLOHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108I| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108I| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCARGDIHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCARGDIHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1861| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1861| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5111| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5111| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.7.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-127| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-127| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14290| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14290| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19854| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19854| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14904| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14904| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5205| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5205| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NACGLCTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NACGLCTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KETOGLUTREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOGLUTREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-20| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-20| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12104| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12104| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TARTRATE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TARTRATE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-261| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-261| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMINOCYL-TRNA-HYDROLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINOCYL-TRNA-HYDROLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7270| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7270| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTSEMIALDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTSEMIALDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3901| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3901| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-312| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-312| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15147| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15147| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETYL-COA-ACETYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYL-COA-ACETYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-344| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-344| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6941| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6941| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NICOTINATEPRIBOSYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICOTINATEPRIBOSYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-361| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-361| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THTOREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THTOREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-41| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-41| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARYLSULFAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARYLSULFAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-81| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-81| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4401| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4401| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14480| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14480| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5076| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5076| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-3521| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3521| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15358| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15358| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-203| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-203| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ORNDECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ORNDECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LUMAZINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LUMAZINESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-235| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-235| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12540| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12540| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-CYTIDYLYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-CYTIDYLYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-275| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-275| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BARA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BARA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-963| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-963| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-446| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-446| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOHMETRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOHMETRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16003| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16003| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-466| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-466| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEPDEPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPDEPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADDALT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADDALT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7199| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7199| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6982| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6982| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPACYLGLCNACDEACETYL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPACYLGLCNACDEACETYL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1701| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1701| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CDPDIGLYPYPHOSPHA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPDIGLYPYPHOSPHA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-271| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-271| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-491| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-491| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.26.12-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.12-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5121| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5121| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7221| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7221| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16660| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16660| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1982| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1982| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7607| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7607| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHENYLPYRUVATE-TAUTOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENYLPYRUVATE-TAUTOMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-23-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-23-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URKI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URKI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-505| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-505| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12872| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12872| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CPXA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CPXA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-56-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-56-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5185| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5185| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-5-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-5-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-524| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-524| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GST-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GST-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16938| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16938| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-546| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-546| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PNKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AIRS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AIRS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-566| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-566| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7010| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7010| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DAHPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DAHPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-586| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-586| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5220| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5220| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-305| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-305| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15740| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15740| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.11.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17473| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17473| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-607| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-607| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROPIONYL-COA-CARBOXY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROPIONYL-COA-CARBOXY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14810| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14810| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-105| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-105| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8460| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8460| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYGUANPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYGUANPHOSPHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-114| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-114| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5295| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5295| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-131| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-131| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13747| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13747| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17725| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17725| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-157| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-157| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRIMSYN1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIMSYN1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCSEMIALDDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCSEMIALDDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-218| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-218| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HEMEOSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HEMEOSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5256| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5256| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5391| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5391| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALPHA-AMYL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALPHA-AMYL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-27| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-27| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7068| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7068| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17785| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17785| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-292| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-292| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3601| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3601| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-324| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-324| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.89-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.89-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DMK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMK-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-348| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-348| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5455| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5455| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15123| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15123| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENTG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9025| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9025| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17846| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17846| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-364| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-364| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOSYLPYRIMIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOSYLPYRIMIDINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAG6PDEACET-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAG6PDEACET-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-56| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-56| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14090| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14090| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DXS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DXS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-90| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-90| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6367| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6367| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIOESTER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOESTER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-206| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-206| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYDROXYLAMINE-REDUCTASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDROXYLAMINE-REDUCTASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17944| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17944| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-240| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-240| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11135| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11135| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARCB717-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCB717-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8638| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8638| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7115| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7115| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FORMYLTHFDEFORMYL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FORMYLTHFDEFORMYL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-278| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-278| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6479| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6479| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4222| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4222| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-449| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-449| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.3.1.17-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.3.1.17-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.215-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.215-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-469| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-469| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18550| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18550| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15299| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15299| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7202| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7202| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1321| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11586| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11586| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1741| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1741| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTUROISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTUROISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-LIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-LIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-495| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-495| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14196| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14196| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6518| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6518| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-26-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-26-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-DEHYDROPANTOATE-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-DEHYDROPANTOATE-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANSALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANSALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-509| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-509| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISOLEUCINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOLEUCINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19025| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19025| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-7-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-7-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11791| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11791| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARTATEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTATEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-527| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-527| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7219| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7219| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCARDEHYDRA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCARDEHYDRA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6555| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6555| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5038| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5038| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-550| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-550| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|7KAPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|7KAPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.4.1.78-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.4.1.78-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-570| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-570| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19573| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19573| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15878| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15878| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-589| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-589| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1922| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1922| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11865| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11865| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-610| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-610| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-PEROXIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-PEROXIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14379| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14379| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6722| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6722| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-118| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-118| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.9.1.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.9.1.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-14| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-14| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|L-LACTDEHYDROGFMN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-LACTDEHYDROGFMN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19954| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19954| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-16| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-16| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12275| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12275| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERLEU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERLEU-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-23| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-23| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7283| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7283| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5266| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5266| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6973| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6973| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5101| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5101| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-277| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-277| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETYLORNTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLORNTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.13.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.13.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5330| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5330| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-6081| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6081| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16420| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16420| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-296| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-296| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12753| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12753| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-33| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-33| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GMP-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GMP-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSII-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSII-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-350| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-350| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14500| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14500| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6992| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6992| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19020| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19020| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.3.74-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.3.74-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPSUGARHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPSUGARHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-367| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-367| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LYSOPHOSPHOLIPASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSOPHOSPHOLIPASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7948| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7948| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-61| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-61| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13142| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13142| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHORPYRLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORPYRLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN1-42| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN1-42| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GUANPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANPRIBOSYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-211| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-211| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7023| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7023| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5131| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5131| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-264| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-264| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.15.5-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.15.5-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13519| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13519| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8654| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8654| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16691| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16691| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-280| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-280| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14014| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14014| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-453| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-453| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHAGLYPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHAGLYPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTOLDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTOLDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-474| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-474| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|XANPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XANPRIBOSYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14534| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14534| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7083| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7083| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7205| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7205| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTDEAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTDEAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.6.1.41-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.1.41-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1804| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1804| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5200| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5200| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNPDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNPDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9597| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9597| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-11-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-11-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17010| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17010| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14126| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14126| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PPPGPPHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPPGPPHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SORBITOL-6-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SORBITOL-6-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|INOPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOPHOSPHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-512| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-512| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DCTP-DEAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCTP-DEAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7160| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7160| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5229| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5229| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALANINE-AMINOTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALANINE-AMINOTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.3.3.14-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.3.3.14-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-9-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17632| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17632| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1483| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1483| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-530| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-530| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PSERTRANSAMPYR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PSERTRANSAMPYR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3182| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3182| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14282| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14282| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN66-448| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN66-448| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DGTPTRIPHYDRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DGTPTRIPHYDRO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDPD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-534| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-534| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5359| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5359| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14815| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14815| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7248| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7248| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-556| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-556| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17777| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17777| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOINDEHYDROG-A-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOINDEHYDROG-A-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|QOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MMUM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MMUM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2061| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2061| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-573| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-573| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROOROT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROOROT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14461| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14461| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-592| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-592| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5410| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5410| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SULFOCYS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFOCYS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LEUCYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LEUCYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-614| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-614| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17793| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17793| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-743| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-743| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVIN-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVIN-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMACETOXID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMACETOXID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACYL-COA-HYDROLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYL-COA-HYDROLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121C| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121C| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTDPGLUCDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPGLUCDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-262| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-262| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6256| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6256| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14512| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14512| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-165| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-165| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17916| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17916| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17652| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17652| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10018| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10018| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15129| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15129| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SAMDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SAMDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-238| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-238| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ETHAMLY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ETHAMLY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADOMET-DMK-METHYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADOMET-DMK-METHYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-280| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-280| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6427| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6427| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NARQ-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARQ-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-300| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-300| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-299| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-299| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6450| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6450| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14753| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14753| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-336| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-336| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18232| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18232| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THREONINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREONINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHIONYL-TRNA-FORMYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHIONYL-TRNA-FORMYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6369| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6369| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11409| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11409| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCGLUALDDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCGLUALDDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-353| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-353| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FUMHYDR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUMHYDR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARGININE-N-SUCCINYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGININE-N-SUCCINYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALDOSE1EPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALDOSE1EPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-371| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-371| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6493| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6493| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-68| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-68| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.11.1.15-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.11.1.15-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4301| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4301| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14997| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14997| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-99| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-99| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18737| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18737| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-NH3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-NH3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-214| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-214| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11600| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11600| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15345| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15345| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TETRAACYLDISACC4KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TETRAACYLDISACC4KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-267| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-267| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GDPMANDEHYDRA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPMANDEHYDRA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMP-NUCLEOSID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMP-NUCLEOSID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-284| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-284| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6528| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6528| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OHBUTYRYL-COA-EPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHBUTYRYL-COA-EPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3942| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3942| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-459| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-459| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-OXOPENT-4-ENOATE-HYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OXOPENT-4-ENOATE-HYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15292| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15292| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7185| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7185| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19338| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19338| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TREHALOSE6PSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALOSE6PSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NQOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NQOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-16| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-16| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11838| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11838| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THYMIDYLATE-5-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYMIDYLATE-5-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-478| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-478| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ATPASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARAGHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARAGHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7208| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7208| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6576| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6576| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4641| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4641| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-14-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-14-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.13.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.13.2-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5052| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5052| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15581| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15581| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-498| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-498| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19793| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19793| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OXALOACETATE-TAUTOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALOACETATE-TAUTOMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7242| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7242| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12093| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12093| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15943| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15943| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRNA-PSEUDOURIDINE-SYNTHASE-I-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-PSEUDOURIDINE-SYNTHASE-I-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2162| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2162| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTRNAREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTRNAREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BETA-LACTAMASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETA-LACTAMASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-34-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-34-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6938| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6938| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PANTOTHENATE-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTOTHENATE-KIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5063| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5063| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-515| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-515| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16225| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16225| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2522| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2522| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-3482| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3482| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMUR-ALA-LIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMUR-ALA-LIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PEROXID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEROXID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-537| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-537| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12539| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12539| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-559| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-559| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOCARBOLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOCARBOLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CARBOXYLESTERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARBOXYLESTERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CELLULOSE-SYNTHASE-UDP-FORMING-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CELLULOSE-SYNTHASE-UDP-FORMING-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-576| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-576| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6981| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6981| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5124| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5124| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-596| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-596| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.26.11-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.11-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5114| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5114| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16685| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16685| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7605| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7605| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOR-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-617| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-617| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12871| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12871| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16475| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16475| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UROPORIIIMETHYLTRANSA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UROPORIIIMETHYLTRANSA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108E| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108E| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GSPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CTPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CTPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-123| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-123| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7008| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7008| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URACIL-PRIBOSYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URACIL-PRIBOSYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5189| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5189| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-145| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-145| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.11.18-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.18-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16996| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16996| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-168| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-168| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8348| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8348| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|COBALAMIN5PSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBALAMIN5PSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13548| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13548| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DARAB5PISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARAB5PISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-283| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-283| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HCAMULTI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HCAMULTI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5181| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5181| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5224| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5224| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-30| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-30| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7067| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7067| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17493| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17493| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIMESULFREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIMESULFREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.87-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.87-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16804| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16804| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PROTOPORGENOXI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTOPORGENOXI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-339| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-339| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8999| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8999| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6373| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6373| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14074| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14074| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOENOLPYRUVATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOENOLPYRUVATE-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5304| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5304| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-356| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-356| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYDGLUTSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDGLUTSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17752| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17752| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-377| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-377| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7114| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7114| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|XYLULOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLULOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYROXALTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYROXALTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-72| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-72| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4.3.1.15-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.3.1.15-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDLIPACETRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDLIPACETRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12440| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12440| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTIKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5398| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5398| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-181| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-181| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14188| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14188| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17788| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17788| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-226| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-226| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ISOCIT-CLEAV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCIT-CLEAV-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5213| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5213| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RFFTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RFFTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13163| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13163| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7188| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7188| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-RNA-POLYMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-RNA-POLYMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-270| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-270| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|7-ALPHA-HYDROXYSTEROID-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|7-ALPHA-HYDROXYSTEROID-DEH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17391| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17391| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5507| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5507| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-417| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-417| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1882| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1882| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17886| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17886| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-10| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-10| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14363| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14363| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRIBFAICARPISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRIBFAICARPISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RNA-3-PHOSPHATE-CYCLASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RNA-3-PHOSPHATE-CYCLASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.6.3.39-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.39-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|L-IDONATE-2-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-IDONATE-2-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ENTDB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTDB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-462| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-462| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7280| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7280| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXGALACTKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXGALACTKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-481| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-481| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETYLORNDEACET-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLORNDEACET-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17956| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17956| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7211| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7211| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5289| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5289| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17962| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17962| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1923| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1923| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14497| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14497| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11313| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11313| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-18-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-18-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LYSINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17636| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17636| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FRUCTOKINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FRUCTOKINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-501| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-501| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-986| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-986| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6482| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6482| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7245| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7245| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENOSINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENOSINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRAMKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRAMKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.1.1.271-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.271-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-37-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-37-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-279| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-279| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18703| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18703| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-519| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-519| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14525| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14525| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DHHB-METHYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHHB-METHYLTRANSFER-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11591| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11591| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-540| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-540| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MANNOSE-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNOSE-ISOMERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GART-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GART-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-562| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-562| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SORB6PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SORB6PDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5375| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5375| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6523| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6523| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-579| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-579| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALANINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALANINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-SYNTHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-SYNTHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-601| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-601| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-313| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-313| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17781| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17781| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19253| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19253| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-10| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-10| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14813| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14813| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11833| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11833| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-628| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-628| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MHPHYDROXY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPHYDROXY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|R15-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R15-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUCONOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCONOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108H| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108H| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SULFITE-REDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFITE-REDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6563| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6563| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126B| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126B| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALTRODEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTRODEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIMETHUROPORDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIMETHUROPORDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.6.1.57-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.6.1.57-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CARBPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARBPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3741| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19630| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19630| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153A| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153A| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15127| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15127| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5422| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5422| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12002| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12002| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5203| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5203| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NAPHTHOATE-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAPHTHOATE-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTCYSLIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTCYSLIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-2| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-2| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THREODEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREODEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17797| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17797| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6727| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6727| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-250| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-250| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARGININE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGININE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2TRANSKETO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2TRANSKETO-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-286| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-286| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4281| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4281| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-2043| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2043| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-310| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-310| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15341| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15341| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12444| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12444| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGFAD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGFAD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OHACYL-COA-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHACYL-COA-DEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DUDPKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DUDPKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCOLALD-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLALD-DEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-342| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-342| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TREHALA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6976| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6976| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-360| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-360| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ATP-PYROPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATP-PYROPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6274| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6274| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.21.1-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.1-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6511| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6511| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5051| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5051| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-6321| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6321| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11496| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11496| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15925| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15925| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17930| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17930| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12861| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12861| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-40| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-40| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PANTOATE-BETA-ALANINE-LIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTOATE-BETA-ALANINE-LIG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GPH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-8| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-8| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TYROSINE-AMINOTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TYROSINE-AMINOTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10814| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10814| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6999| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6999| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-202| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-202| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CARBOXYLATE-REDUCTASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARBOXYLATE-REDUCTASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.2.1.21-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.1.21-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-233| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-233| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5108| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5108| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FADSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FADSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8073| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8073| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-274| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-274| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16457| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16457| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13248| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13248| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-445| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-445| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|URA-PHOSPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URA-PHOSPH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10856| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10856| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-12| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-12| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|COBALADENOSYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBALADENOSYLTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-704| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-704| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-465| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-465| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5146| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5146| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FGAMSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FGAMSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.21.102-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.102-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7191| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7191| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16788| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16788| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8770| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8770| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-17| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-17| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOAMIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOAMIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6460| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6460| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14026| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14026| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-490| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-490| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|XYLONATE-DEHYDRATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLONATE-DEHYDRATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSMETB12-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSMETB12-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1981| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1981| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTIDINEKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDINEKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18388| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18388| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7100| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7100| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-20-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-20-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5210| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5210| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-504| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-504| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17330| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17330| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11573| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11573| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9952| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9952| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-5-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-5-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14142| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14142| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-523| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-523| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DCYSDESULF-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCYSDESULF-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|INOSINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINE-NUCLEOSIDASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTOKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTOKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-545| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-545| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5285| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5285| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7167| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7167| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-565| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-565| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17635| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17635| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6509| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6509| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5.99.1.2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.99.1.2-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-585| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-585| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PUTTRANSAM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PUTTRANSAM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-606| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-606| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DHDOGALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHDOGALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.5.1.34-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.5.1.34-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14285| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14285| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-104| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-104| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5364| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5364| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KETOACYLCOATHIOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOACYLCOATHIOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-113| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-113| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17780| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17780| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18999| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18999| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7251| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7251| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ATPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|QUINOPRIBOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QUINOPRIBOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTREDUCTOISOM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTREDUCTOISOM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-130| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-130| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROXYMETVALDEHYDRAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROXYMETVALDEHYDRAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11635| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11635| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2161| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2161| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-156| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-156| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5418| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5418| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14478| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14478| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-21| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-21| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17796| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17796| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLCNACPTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLCNACPTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LTAA-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LTAA-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DALADEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DALADEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNREDUC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNREDUC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-961| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-961| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-267| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-267| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTMPKI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTMPKI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6541| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6541| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACYLPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-291| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-291| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6272| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6272| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2661| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2661| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-320| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-320| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17920| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17920| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.1.1.79-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.79-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14515| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14515| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-347| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-347| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10720| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10720| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MALTODEXGLUCOSID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALTODEXGLUCOSID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-363| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-363| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|F16BDEPHOS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|F16BDEPHOS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19381| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19381| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SERINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SERINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FORMATEDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FORMATEDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|FCLREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FCLREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AICARSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AICARSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-44| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-44| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6459| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6459| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11842| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11842| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-303| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-303| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-86| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-86| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18376| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18376| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14808| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14808| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-205| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-205| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11484| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11484| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLUTAMIDOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMIDOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-EPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-EPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-239| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-239| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GALACTOACETYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTOACETYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SUCCINYLDIAMINOPIMTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINYLDIAMINOPIMTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13403| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13403| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6506| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6506| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6710| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6710| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALLANTOINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLANTOINASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-448| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-448| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|1.5.1.20-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.5.1.20-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3542| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3542| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-14| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-14| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-18819| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18819| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.7.8-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.8-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15121| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15121| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-468| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-468| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11633| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11633| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NADPYROPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADPYROPHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7201| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7201| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GKI-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GKI-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19921| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19921| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN3-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN3-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1721| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1721| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6532| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6532| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ANTHRANSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ANTHRANSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-493| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-493| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.1.1.77-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.77-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12195| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12195| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4121| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4121| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-25-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-25-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19362| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19362| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15297| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15297| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-508| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-508| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-11841| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11841| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYCDEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCDEH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NUCLEOTIDE-PYROPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOTIDE-PYROPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ABC-64-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-64-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLURS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLURS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-277| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-277| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-526| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-526| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6708| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6708| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6948| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6948| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ASPARTATE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTATE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|2.7.7.60-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.60-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-19920| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19920| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15744| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15744| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12149| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12149| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|OXAMATE-CARBAMOYLTRANSFERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXAMATE-CARBAMOYLTRANSFERASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYC3PDEHYDROGBIOSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYC3PDEHYDROGBIOSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-4821| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-4821| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TRYPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6945| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6945| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|BIS5-ADENOSYL-TRIPHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BIS5-ADENOSYL-TRIPHOSPHATASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12587| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12587| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5074| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5074| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-3641| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3641| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16286| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16286| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12583| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12583| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOXIII-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXIII-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PGLYCDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GLYOXII-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXII-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6984| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6984| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6985| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6985| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CHORISMATE-SYNTHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORISMATE-SYNTHASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.26.4-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.4-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5127| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5127| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7632| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7632| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.1.26.5-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.5-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-16689| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16689| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12886| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12886| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PHOSMANMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSMANMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-II-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-II-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-7682| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7682| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|VALINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|VALINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7013| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7013| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYSTEINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTEINE--TRNA-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.11.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.9-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-12895| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12895| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5195| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5195| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8487| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8487| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17008| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17008| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13853| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13853| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|GTPPYPHOSKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTPPYPHOSKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PPENTOMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPENTOMUT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTALDEHYD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTALDEHYD-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DARABKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABKIN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7075| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7075| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7014| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7014| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5227| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5227| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17928| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17928| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.23.43-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.23.43-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17630| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17630| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17910| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17910| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9310| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9310| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.13.18-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.18-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PRTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14112| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14112| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DETHIOBIOTIN-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DETHIOBIOTIN-SYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HYPOXANPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYPOXANPRIBOSYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-8506| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8506| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5311| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5311| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7122| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7122| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17775| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17775| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5-FORMYL-THF-CYCLO-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-FORMYL-THF-CYCLO-LIGASE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-13854| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13854| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|PYRUVATEDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUVATEDECARB-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1382| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1382| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATESYNTH-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14251| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14251| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|HISTAMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTAMINOTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5408| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5408| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDGALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDGALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17791| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17791| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7229| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7229| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7078| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7078| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RHAMNULPALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RHAMNULPALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETALD-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETALD-DEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DTDPDEHYDRHAMEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPDEHYDRHAMEPIM-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2001| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2001| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|3.4.24.55-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.24.55-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-5515| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5515| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14393| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14393| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-17905| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17905| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LACTALDDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LACTALDDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-9311| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9311| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-10016| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10016| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7291| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7291| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ERYTH4PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ERYTH4PDEHYDROG-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACNEULY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACNEULY-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14113| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14113| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-6389| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6389| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2584| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2584| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14503| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14503| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|IGPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IGPSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|LYXK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYXK-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXNMETA-12671| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXNMETA-12671| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7139| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7139| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ADENPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENPRIBOSYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2941| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2941| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|5-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-NUCLEOTID-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14569| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14569| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MERCAPYSTRANS-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1401| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SPERMIDINESYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7049| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14255| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1130| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3221| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UBIQUINOL-OX-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14882| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDO-8PPHOSPHAT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMK-FE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSBDC-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TAGAALDOL-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7230| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MEN-FE-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINEPHEN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7048| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-384| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETATE--COA-LIGASE-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7096| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15139| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5068| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2022| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7310| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREOSPON-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTC-RED-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGSUCCINSYN-RXN| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14394| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3141| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4342| ))\n", + "cofactors-and-pgroups-of-enzrxn\n", + "(cofactors-and-pgroups-of-enzrxn '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " lst.append(ecoli.cofactors_and_pgroups_of_enzrxn(enzrxn = enzrxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-15348| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-15348| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|LACTALDREDUCT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|LACTALDREDUCT-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|PFLDEACTIV-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PFLDEACTIV-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|OHMETPYRKIN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|OHMETPYRKIN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7094| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7094| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|TRIOSEPISOMERIZATION-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TRIOSEPISOMERIZATION-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7298| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7298| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-1137| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-1137| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|BADH-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|BADH-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|DMKCYT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DMKCYT-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-5061| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5061| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ACONITATE-DELTA-ISOMERASE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACONITATE-DELTA-ISOMERASE-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|FES-OX-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|FES-OX-RXN| t ))\n", + "enzrxn-activators\n", + 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(enzrxn-activators '|TRANS-RXN0-564| t ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-17795| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-17795| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-15119| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-15119| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|TRANS-RXN0-584| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TRANS-RXN0-584| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14065| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14065| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RIBOFLAVINSYNDEAM-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RIBOFLAVINSYNDEAM-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|TRANS-RXN0-604| t )\n", + "(with-organism (:org-id '|ECOLI|) 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"enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7078| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7078| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RHAMNULPALDOL-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RHAMNULPALDOL-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ACETALD-DEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACETALD-DEHYDROG-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|DTDPDEHYDRHAMEPIM-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DTDPDEHYDRHAMEPIM-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-2001| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2001| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|3.4.24.55-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|3.4.24.55-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-5515| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5515| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14393| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14393| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-17905| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-17905| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|LACTALDDEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|LACTALDDEHYDROG-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-9311| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-9311| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-10016| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-10016| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7291| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7291| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ERYTH4PDEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ERYTH4PDEHYDROG-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ACNEULY-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACNEULY-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14113| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14113| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-6389| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6389| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-2584| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2584| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14503| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14503| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|IGPSYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|IGPSYN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|LYXK-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|LYXK-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXNMETA-12671| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXNMETA-12671| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7139| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7139| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ADENPRIBOSYLTRAN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ADENPRIBOSYLTRAN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-2941| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2941| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|5-NUCLEOTID-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|5-NUCLEOTID-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14569| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14569| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|MERCAPYSTRANS-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MERCAPYSTRANS-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-1401| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-1401| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|SPERMIDINESYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|SPERMIDINESYN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7049| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7049| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ALCOHOL-DEHYDROG-GENERIC-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ALCOHOL-DEHYDROG-GENERIC-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14255| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14255| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-1130| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-1130| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-3221| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-3221| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|UBIQUINOL-OX-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|UBIQUINOL-OX-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14882| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14882| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|KDO-8PPHOSPHAT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|KDO-8PPHOSPHAT-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|DMK-FE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DMK-FE-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|N-ACETYLGLUTPREDUCT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|N-ACETYLGLUTPREDUCT-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|DSBDC-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DSBDC-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|TAGAALDOL-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TAGAALDOL-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7230| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7230| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|MEN-FE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MEN-FE-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|AMINEPHEN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|AMINEPHEN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7048| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7048| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-384| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-384| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|ACETATE--COA-LIGASE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACETATE--COA-LIGASE-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7096| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7096| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-15139| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-15139| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-5068| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-5068| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|NICONUCADENYLYLTRAN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|NICONUCADENYLYLTRAN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-2022| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2022| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-7310| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7310| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|THREOSPON-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|THREOSPON-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|CYTC-RED-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|CYTC-RED-RXN| t ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzrxn-activators\n", + "(enzrxn-activators '|ARGSUCCINSYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ARGSUCCINSYN-RXN| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN-14394| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14394| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-3141| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-3141| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|RXN0-4342| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-4342| t ))\n", + "enzrxn-activators\n", + "(enzrxn-activators '|DSBD-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DSBD-RXN| t ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "er\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "phys-relevant-only?\n", + "Optional If true, then only return activators that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_activators(enzrxn = enzrxn, phys_relevant_only=True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-15348| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-15348| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|LACTALDREDUCT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|LACTALDREDUCT-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|PFLDEACTIV-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PFLDEACTIV-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|OHMETPYRKIN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors 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+ "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-17630| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17630| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-17910| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17910| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-9310| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-9310| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|3.4.13.18-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|3.4.13.18-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|PRTRANS-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PRTRANS-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14112| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14112| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DETHIOBIOTIN-SYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DETHIOBIOTIN-SYN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|HYPOXANPRIBOSYLTRAN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|HYPOXANPRIBOSYLTRAN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-8506| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-8506| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-5311| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5311| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7122| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7122| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-17775| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17775| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|5-FORMYL-THF-CYCLO-LIGASE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|5-FORMYL-THF-CYCLO-LIGASE-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-13854| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-13854| t ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|PYRUVATEDECARB-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PYRUVATEDECARB-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-1382| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-1382| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DIHYDROFOLATESYNTH-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DIHYDROFOLATESYNTH-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14251| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14251| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|HISTAMINOTRANS-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|HISTAMINOTRANS-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-5408| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5408| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|KDGALDOL-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|KDGALDOL-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-17791| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17791| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7229| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7229| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7078| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7078| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RHAMNULPALDOL-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RHAMNULPALDOL-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ACETALD-DEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ACETALD-DEHYDROG-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DTDPDEHYDRHAMEPIM-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DTDPDEHYDRHAMEPIM-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-2001| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2001| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|3.4.24.55-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|3.4.24.55-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-5515| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5515| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14393| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14393| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-17905| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17905| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|LACTALDDEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|LACTALDDEHYDROG-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-9311| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-9311| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-10016| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-10016| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7291| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7291| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ERYTH4PDEHYDROG-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ERYTH4PDEHYDROG-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ACNEULY-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ACNEULY-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14113| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14113| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-6389| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-6389| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-2584| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2584| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14503| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14503| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|IGPSYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|IGPSYN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|LYXK-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|LYXK-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXNMETA-12671| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXNMETA-12671| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7139| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7139| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ADENPRIBOSYLTRAN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ADENPRIBOSYLTRAN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-2941| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2941| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|5-NUCLEOTID-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|5-NUCLEOTID-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14569| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14569| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|MERCAPYSTRANS-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MERCAPYSTRANS-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-1401| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-1401| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|SPERMIDINESYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|SPERMIDINESYN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7049| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7049| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ALCOHOL-DEHYDROG-GENERIC-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ALCOHOL-DEHYDROG-GENERIC-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14255| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14255| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-1130| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-1130| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-3221| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-3221| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|UBIQUINOL-OX-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|UBIQUINOL-OX-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14882| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14882| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|KDO-8PPHOSPHAT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|KDO-8PPHOSPHAT-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DMK-FE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DMK-FE-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|N-ACETYLGLUTPREDUCT-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|N-ACETYLGLUTPREDUCT-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DSBDC-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DSBDC-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|TAGAALDOL-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|TAGAALDOL-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7230| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7230| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|MEN-FE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MEN-FE-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|AMINEPHEN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|AMINEPHEN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7048| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7048| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-384| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-384| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ACETATE--COA-LIGASE-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ACETATE--COA-LIGASE-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7096| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7096| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-15139| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-15139| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-5068| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-5068| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|NICONUCADENYLYLTRAN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|NICONUCADENYLYLTRAN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-2022| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2022| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-7310| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7310| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|THREOSPON-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|THREOSPON-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|CYTC-RED-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|CYTC-RED-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|ARGSUCCINSYN-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ARGSUCCINSYN-RXN| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN-14394| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14394| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-3141| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-3141| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|RXN0-4342| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-4342| t ))\n", + "enzrxn-inhibitors\n", + "(enzrxn-inhibitors '|DSBD-RXN| t )\n", + "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DSBD-RXN| t ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_inhibitors(enzrxn = enzrxn, phys_relevant_only = True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN-15348| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-15348| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|LACTALDREDUCT-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|LACTALDREDUCT-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|PFLDEACTIV-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PFLDEACTIV-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|OHMETPYRKIN-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|OHMETPYRKIN-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN0-7094| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7094| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN0-7298| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7298| 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"(pathways-of-enzrxn '|RXN0-7310| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7310| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|THREOSPON-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|THREOSPON-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|CYTC-RED-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|CYTC-RED-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|ARGSUCCINSYN-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ARGSUCCINSYN-RXN| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN-14394| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-14394| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN0-3141| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-3141| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|RXN0-4342| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-4342| :include-super-pwys? nil))\n", + "pathways-of-enzrxn\n", + "(pathways-of-enzrxn '|DSBD-RXN| :include-super-pwys? nil)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|DSBD-RXN| :include-super-pwys? nil))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "include-super-pwys?\n", + "Keyword, Optional If non-nil, then not only will the direct pathways in which \n", + "enzrxn is associated in be returned, but also any enclosing super-pathways. If \n", + "enzrxn is associated with a reaction that is directly associated with a \n", + "super-pathway, then the function might return super-pathways even if this option \n", + "is nil.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.pathways_of_enzrxn(enzrxn = enzrxn, include_super_pwys = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "all-rxns\n", + "(all-rxns :all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns :all ))\n", + "all-rxns\n", + "(all-rxns :metab-smm )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns :metab-smm ))\n", + "pathway-allows-enzrxn\\?\n", + "(pathway-allows-enzrxn\\? '|PWY0-1347| '|RXN-15348| '|RXN-15348| '|ECOLI| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-allows-enzrxn\\? '|PWY0-1347| '|RXN-15348| '|RXN-15348| '|ECOLI| ))\n" + ] + }, + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1640\u001b[0m \t\t\"\"\"\n\u001b[1;32m 1641\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1642\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn\\\\?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1643\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 375\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 376\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 377\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 367\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 368\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 369\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 370\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 357\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m') '\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mquery\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 358\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 359\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 360\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 361\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "single-species\n", + "Optional An instance of the class |Organisms| If set, then enzrxn has the \n", + "further stricture that it must be an enzymatic reaction present in the organism \n", + "specified by the value passed to single‑species.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " for rxn1 in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " for rxn2 in ecoli.all_rxns(type_of_reactions = 'metab-smm'):\n", + " lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n", + " pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Genes.ipynb b/examples/ptools API - Operations on Genes.ipynb new file mode 100644 index 0000000..3a43670 --- /dev/null +++ b/examples/ptools API - Operations on Genes.ipynb @@ -0,0 +1,775 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[u'|META|', u'|ECOLI|']\n", + "class-name-p\n", + "(class-name-p \"genes\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"genes\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Genes| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Genes| ))\n", + "get-class\n", + "(get-class |Genes| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Genes| ))\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "genes = [x.frameid for x in ecoli.genes.instances][0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "gene-p\n", + "(gene-p '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (gene-p '|EG11414| ))\n", + "gene-p\n", + "(gene-p '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (gene-p '|EG11127| ))\n", + "[u'|Genes|', u'|Genes|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.gene_p(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-gene\n", + "(enzymes-of-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-gene '|EG11414| ))\n", + "enzymes-of-gene\n", + "(enzymes-of-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-gene '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.enzymes_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-products-of-gene\n", + "(all-products-of-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (all-products-of-gene '|EG11414| ))\n", + "all-products-of-gene\n", + "(all-products-of-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (all-products-of-gene '|EG11127| ))\n", + "[[u'|EG11414-MONOMER|', u'|CPLX0-7910|', u'|CPLX0-3803|'], [u'|EG11127-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.all_products_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reactions-of-gene\n", + "(reactions-of-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-gene '|EG11414| ))\n", + "reactions-of-gene\n", + "(reactions-of-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-gene '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.reactions_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pathways-of-gene\n", + "(pathways-of-gene '|EG11414| :include-super-pwys? t :include-gene-prod-as-substrate? t)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-gene '|EG11414| :include-super-pwys? t :include-gene-prod-as-substrate? t))\n", + "pathways-of-gene\n", + "(pathways-of-gene '|EG11127| :include-super-pwys? t :include-gene-prod-as-substrate? t)\n", + "(with-organism (:org-id '|ECOLI|) (pathways-of-gene '|EG11127| :include-super-pwys? t :include-gene-prod-as-substrate? t))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.pathways_of_gene(gene, True, True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chromosome-of-gene\n", + "(chromosome-of-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-gene '|EG11414| ))\n", + "chromosome-of-gene\n", + "(chromosome-of-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-gene '|EG11127| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.chromosome_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "unmodified-gene-product\n", + "(unmodified-gene-product '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-gene-product '|EG11414| ))\n", + "unmodified-gene-product\n", + "(unmodified-gene-product '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-gene-product '|EG11127| ))\n", + "[u'|EG11414-MONOMER|', u'|EG11127-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.unmodified_gene_product(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "unmodified-gene-products\n", + "(unmodified-gene-products '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-gene-products '|EG11414| ))\n", + "unmodified-gene-products\n", + "(unmodified-gene-products '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-gene-products '|EG11127| ))\n", + "[[u'|EG11414-MONOMER|'], [u'|EG11127-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.unmodified_gene_products(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "next-gene-on-replicon\n", + "(next-gene-on-replicon '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (next-gene-on-replicon '|EG11414| ))\n", + "next-gene-on-replicon\n", + "(next-gene-on-replicon '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (next-gene-on-replicon '|EG11127| ))\n", + "[u'|EG10850|', u'|EG11024|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.next_gene_on_replicon(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "previous-gene-on-replicon\n", + "(previous-gene-on-replicon '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (previous-gene-on-replicon '|EG11414| ))\n", + "previous-gene-on-replicon\n", + "(previous-gene-on-replicon '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (previous-gene-on-replicon '|EG11127| ))\n", + "[u'|G7950|', u'|EG11126|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.previous_gene_on_replicon(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes are the same.\n", + "adjacent-genes?\n", + "(adjacent-genes? '|EG11414| '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (adjacent-genes? '|EG11414| '|EG11127| ))\n", + "adjacent-genes?\n", + "(adjacent-genes? '|EG11127| '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (adjacent-genes? '|EG11127| '|EG11414| ))\n", + "genes are the same.\n", + "[None, False, False, None]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene1 in genes:\n", + " for gene2 in genes:\n", + " lst.append(ecoli.adjacent_genes_p(gene1, gene2))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes are the same.\n", + "neighboring-genes-p\n", + "(neighboring-genes-p '|EG11414| '|EG11127| 10 )\n", + "(with-organism (:org-id '|ECOLI|) (neighboring-genes-p '|EG11414| '|EG11127| 10 ))\n", + "neighboring-genes-p\n", + "(neighboring-genes-p '|EG11127| '|EG11414| 10 )\n", + "(with-organism (:org-id '|ECOLI|) (neighboring-genes-p '|EG11127| '|EG11414| 10 ))\n", + "genes are the same.\n", + "[None, False, False, None]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene1 in genes:\n", + " for gene2 in genes:\n", + " lst.append(ecoli.neighboring_genes_p(gene1, gene2))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "gene-clusters\n", + "(gene-clusters '(|EG11414| |EG11127|) 4000 )\n", + "(with-organism (:org-id '|ECOLI|) (gene-clusters '(|EG11414| |EG11127|) 4000 ))\n" + ] + }, + { + "data": { + "text/plain": [ + "{u'|EG11127|': [u'|EG11414|']}" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.gene_clusters(genes, 4000)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rna-coding-gene?\n", + "(rna-coding-gene? '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (rna-coding-gene? '|EG11414| ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for gene in genes:\n", + " lst.append(ecoli.rna_coding_gene(gene=gene))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "protein-coding-gene?\n", + "(protein-coding-gene? '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (protein-coding-gene? '|EG11414| ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for gene in genes:\n", + " lst.append(ecoli.protein_coding_gene(gene=gene))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pseudo-gene-p\n", + "(pseudo-gene-p '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (pseudo-gene-p '|EG11414| ))\n", + "pseudo-gene-p\n", + "(pseudo-gene-p '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (pseudo-gene-p '|EG11127| ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.pseudo_gene_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "phantom-gene-p\n", + "(phantom-gene-p '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (phantom-gene-p '|EG11414| ))\n", + "phantom-gene-p\n", + "(phantom-gene-p '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (phantom-gene-p '|EG11127| ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.phantom_gene_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dna-binding-site-p\n", + "(dna-binding-site-p '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (dna-binding-site-p '|EG11414| ))\n", + "dna-binding-site-p\n", + "(dna-binding-site-p '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (dna-binding-site-p '|EG11127| ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.dna_binding_site_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "terminatorp\n", + "(terminatorp '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (terminatorp '|EG11414| ))\n", + "terminatorp\n", + "(terminatorp '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (terminatorp '|EG11127| ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.terminator_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "operon-of-gene\n", + "(operon-of-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (operon-of-gene '|EG11414| ))\n", + "operon-of-gene\n", + "(operon-of-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (operon-of-gene '|EG11127| ))\n", + "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-36411|', u'|TU0-13193|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.operon_of_gene(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-in-same-operon\n", + "(genes-in-same-operon '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-in-same-operon '|EG11414| ))\n", + "genes-in-same-operon\n", + "(genes-in-same-operon '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-in-same-operon '|EG11127| ))\n", + "[[u'|EG12115|', u'|EG10850|', u'|EG11414|'], [u'|EG11125|', u'|EG11126|', u'|EG11127|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_in_same_operon(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "gene-transcription-units\n", + "(gene-transcription-units '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (gene-transcription-units '|EG11414| ))\n", + "gene-transcription-units\n", + "(gene-transcription-units '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (gene-transcription-units '|EG11127| ))\n", + "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-13193|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.gene_transcription_units(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cotranscribed-genes\n", + "(cotranscribed-genes '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (cotranscribed-genes '|EG11414| ))\n", + "cotranscribed-genes\n", + "(cotranscribed-genes '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (cotranscribed-genes '|EG11127| ))\n", + "[[u'|EG12115|', u'|EG10850|'], [u'|EG11125|', u'|EG11126|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.cotranscribed_genes(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "terminators-affecting-gene\n", + "(terminators-affecting-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (terminators-affecting-gene '|EG11414| ))\n", + "terminators-affecting-gene\n", + "(terminators-affecting-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (terminators-affecting-gene '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.terminators_affecting_gene(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chromosome-of-object\n", + "(chromosome-of-object '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-object '|EG11414| ))\n", + "chromosome-of-object\n", + "(chromosome-of-object '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-object '|EG11127| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.chromosome_of_object(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Pathways.ipynb b/examples/ptools API - Operations on Pathways.ipynb new file mode 100644 index 0000000..7a4cca0 --- /dev/null +++ b/examples/ptools API - Operations on Pathways.ipynb @@ -0,0 +1,11390 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[u'|META|', u'|ECOLI|']\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways :all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways :all t ))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1347| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1347| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1474| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1474| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6690| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6690| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1348| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1348| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5162| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5162| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1352| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1352| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1505| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1505| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1355| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1355| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|2PHENDEG-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|2PHENDEG-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1465| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1465| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|TRESYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TRESYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PANTO-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PANTO-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1356| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1356| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| :sorted? 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t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1512| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1512| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1577| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1577| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5123| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5123| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1313| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1313| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6387| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6387| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PYRIDNUCSAL-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDNUCSAL-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1578| :sorted? 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t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7971| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7971| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1534| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1534| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6952| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6952| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1518| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1518| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7184| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7184| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1584| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1584| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6038| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6038| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PYRIDNUCSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDNUCSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1585| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1585| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-981| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-981| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1495| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1495| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7181| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7181| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7801| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7801| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PYRUVDEHYD-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRUVDEHYD-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5509| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5509| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5350| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5350| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1559| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1559| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ALKANEMONOX-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ALKANEMONOX-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|HOMOSER-METSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HOMOSER-METSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6153| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6153| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1535| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1535| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7206| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7206| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|AST-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|AST-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5340| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5340| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-823| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-823| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-541| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-541| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|THREONINE-DEG2-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|THREONINE-DEG2-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5971| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5971| :sorted? t))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5436| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5436| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7197| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7197| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|THRDLCTCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|THRDLCTCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1533| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1533| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5437| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5437| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|TRNA-CHARGING-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TRNA-CHARGING-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|LCYSDEG-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|LCYSDEG-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6703| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6703| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1517| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1517| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GLYCLEAV-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYCLEAV-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GALACTARDEG-PWY| :sorted? 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t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7193| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7193| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ALANINE-SYN2-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ALANINE-SYN2-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1317| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1317| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|LIPA-CORESYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|LIPA-CORESYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1470| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1470| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1315| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1315| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|SERSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SERSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1280| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1280| :sorted? t))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5698| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5698| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|FAO-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|FAO-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7344| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7344| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7187| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7187| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1503| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1503| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GLUAMCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUAMCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1264| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1264| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ASPARTATESYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ASPARTATESYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1221| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1221| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7343| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7343| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|NAGLIPASYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|NAGLIPASYN-PWY| :sorted? 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t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-1269| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GALACTITOLCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTITOLCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1481| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1481| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|IDNCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|IDNCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-4261| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-4261| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1182| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1182| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|HISTSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HISTSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|TREDEGLOW-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TREDEGLOW-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-2161| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-2161| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|DTDPRHAMSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DTDPRHAMSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1506| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1506| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1306| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1306| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ACETOACETATE-DEG-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ACETOACETATE-DEG-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ENTNER-DOUDOROFF-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ENTNER-DOUDOROFF-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6614| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6614| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|DAPLYSINESYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DAPLYSINESYN-PWY| :sorted? t))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-of-pathway\n", + "(genes-of-pathway '|RHAMCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|RHAMCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|1CMET2-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|1CMET2-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1590| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1590| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7315| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7315| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GLYCOGENSYNTH-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYCOGENSYNTH-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GALACTCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|DARABCATK12-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DARABCATK12-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1485| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1485| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1338| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1338| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6543| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6543| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|ARABCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ARABCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-661| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-661| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1514| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1514| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7242| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7242| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-43| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-43| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1324| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1324| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GLUCONEO-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUCONEO-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|XYLCAT-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|XYLCAT-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-662| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-662| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|SORBDEG-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SORBDEG-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1303| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1303| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1492| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1492| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-301| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-301| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|GALACTMETAB-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTMETAB-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-5852| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5852| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PLPSAL-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PLPSAL-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-321| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-321| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6608| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6608| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-4121| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-4121| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1519| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1519| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6961| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6961| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|SALVADEHYPOX-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SALVADEHYPOX-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PYRIDOXSYN-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDOXSYN-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6617| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6617| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1591| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1591| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1497| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1497| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1507| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1507| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-6556| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6556| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1588| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1588| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PROPIONMET-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PROPIONMET-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1295| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1295| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|RIBOSYN2-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|RIBOSYN2-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1597| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1597| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY-7195| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7195| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1458| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1458| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1321| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1321| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1500| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1500| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|HCAMHPDEG-PWY| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HCAMHPDEG-PWY| :sorted? t))\n", + "genes-of-pathway\n", + "(genes-of-pathway '|PWY0-1336| :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1336| :sorted? t))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|EG12082|',\n", + " u'|EG12088|',\n", + " u'|EG12090|',\n", + " u'|EG12091|',\n", + " u'|EG12092|',\n", + " u'|EG11773|',\n", + " u'|EG12093|',\n", + " u'|EG12089|',\n", + " u'|EG12087|',\n", + " u'|EG11774|',\n", + " u'|EG12086|',\n", + " u'|EG12084|',\n", + " u'|EG12083|',\n", + " u'|EG10330|',\n", + " u'|EG10331|',\n", + " u'|EG10332|',\n", + " u'|EG10333|']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "sorted?\n", + "Keyword, Optional If true, the genes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = 'all', base = True):\n", + " lst.append(ecoli.genes_of_pathway(pwy = pwy, sorted = True))\n", + "lst[-1]\n", + "\n", + "# sorted arg doesn't work because malformed key. sorted changed to sorted?" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1347| :experimental-only? 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t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1338| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1338| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-6543| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6543| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|ARABCAT-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|ARABCAT-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-661| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-661| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1514| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1514| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-7242| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-7242| :experimental-only? t :sorted? t))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-43| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-43| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1324| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1324| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|GLUCONEO-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|GLUCONEO-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|XYLCAT-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|XYLCAT-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-662| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-662| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|SORBDEG-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|SORBDEG-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1303| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1303| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1492| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1492| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-301| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-301| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|GALACTMETAB-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|GALACTMETAB-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-5852| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-5852| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PLPSAL-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PLPSAL-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-321| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-321| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-6608| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6608| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-4121| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-4121| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1519| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1519| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-6961| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6961| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|SALVADEHYPOX-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|SALVADEHYPOX-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PYRIDOXSYN-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PYRIDOXSYN-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-6617| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6617| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1591| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1591| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1497| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1497| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1507| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1507| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-6556| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6556| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1588| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1588| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PROPIONMET-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PROPIONMET-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1295| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1295| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|RIBOSYN2-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|RIBOSYN2-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1597| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1597| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY-7195| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-7195| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1458| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1458| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1321| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1321| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1500| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1500| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|HCAMHPDEG-PWY| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|HCAMHPDEG-PWY| :experimental-only? t :sorted? t))\n", + "enzymes-of-pathway\n", + "(enzymes-of-pathway '|PWY0-1336| :experimental-only? t :sorted? t)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1336| :experimental-only? t :sorted? t))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|NADH-DHI-CPLX|', u'|FUMARATE-REDUCTASE|']" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "sorted?\n", + "Keyword, Optional If true, the enzymes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.enzymes_of_pathway(pwy = pwy, sorted = True, experimental_only = True))\n", + "lst[-1]\n", + "\n", + "# same as previous function" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1347| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1474| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1474| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-6690| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6690| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1348| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1348| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-5162| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1352| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1352| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1505| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1505| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1355| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1355| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|2PHENDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|2PHENDEG-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1465| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|TRESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|TRESYN-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PANTO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PANTO-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1356| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1356| ))\n", + "compounds-of-pathway\n", + 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))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|XYLCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|XYLCAT-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-662| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-662| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|SORBDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|SORBDEG-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1303| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1303| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1492| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1492| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-301| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-301| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|GALACTMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|GALACTMETAB-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-5852| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-5852| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PLPSAL-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PLPSAL-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-321| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-321| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-6608| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6608| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-4121| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-4121| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1519| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1519| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-6961| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6961| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|SALVADEHYPOX-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|SALVADEHYPOX-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PYRIDOXSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PYRIDOXSYN-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-6617| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6617| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1591| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1591| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1497| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1497| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1507| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1507| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6556| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1588| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1588| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PROPIONMET-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PROPIONMET-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1295| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1295| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|RIBOSYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|RIBOSYN2-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1597| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1597| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-7195| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1458| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1458| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1321| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1500| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1500| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|HCAMHPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|HCAMHPDEG-PWY| ))\n", + "compounds-of-pathway\n", + "(compounds-of-pathway '|PWY0-1336| )\n", + "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1336| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|FUM|',\n", + " u'|SUC|',\n", + " u'|Menaquinones|',\n", + " u'|Menaquinols|',\n", + " u'|E-|',\n", + " u'|PROTON|',\n", + " u'|NAD|',\n", + " u'|NADH|']" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.compounds_of_pathway(pwy = pwy))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1347| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1474| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1474| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6690| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6690| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1348| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1348| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5162| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1352| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1352| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1505| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1505| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1355| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1355| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|2PHENDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|2PHENDEG-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1465| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|TRESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|TRESYN-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PANTO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PANTO-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1356| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1356| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1483| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1483| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1573| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1573| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1586| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1586| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|GLUCONSUPER-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLUCONSUPER-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1576| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1576| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|GLYCEROLMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLYCEROLMETAB-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1512| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1512| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1577| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1577| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-5123| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5123| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1313| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1313| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6387| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6387| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PYRIDNUCSAL-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRIDNUCSAL-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1578| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1578| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1490| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1490| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1581| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1581| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY3O-4106| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY3O-4106| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|KDOSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|KDOSYN-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7761| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7761| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1582| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1582| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7971| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7971| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1534| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1534| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6952| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6952| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1518| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1518| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7184| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7184| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1584| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1584| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6038| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6038| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PYRIDNUCSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRIDNUCSYN-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1585| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1585| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-981| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-981| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1495| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1495| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7181| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7181| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7801| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7801| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PYRUVDEHYD-PWY| 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(:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6611| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6892| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6892| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-5194| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5194| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1391| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1391| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1554| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1554| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PROSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PROSYN-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6609| )\n", + "(with-organism (:org-id 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'|PWY0-1314| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1314| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1527| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1527| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|OXIDATIVEPENT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|OXIDATIVEPENT-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7193| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7193| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|ALANINE-SYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ALANINE-SYN2-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1317| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1317| ))\n", + "substrates-of-pathway\n", + 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"(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1507| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6556| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1588| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1588| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PROPIONMET-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PROPIONMET-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1295| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1295| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|RIBOSYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|RIBOSYN2-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1597| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1597| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7195| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1458| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1458| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1321| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1500| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1500| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|HCAMHPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|HCAMHPDEG-PWY| ))\n", + "substrates-of-pathway\n", + "(substrates-of-pathway '|PWY0-1336| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1336| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|NADH|',\n", + " u'|Menaquinones|',\n", + " u'|Menaquinols|',\n", + " u'|PROTON|',\n", + " u'|TRIMETHYLAMINE-N-O|'],\n", + " [u'|TRIMETHYLAMINE-N-O|', u'|NADH|'],\n", + " [u'|NAD|',\n", + " u'|Menaquinols|',\n", + " u'|PROTON|',\n", + " u'|TRIMETHYLAMINE|',\n", + " u'|WATER|',\n", + " u'|Menaquinones|'],\n", + " [u'|WATER|', u'|TRIMETHYLAMINE|', u'|NAD|']]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.substrates_of_pathway(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1347| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1474| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1474| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6690| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6690| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1348| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1348| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5162| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1352| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1352| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1505| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1505| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1355| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1355| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|2PHENDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|2PHENDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1465| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|TRESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TRESYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PANTO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PANTO-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1356| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1356| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1483| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1483| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1573| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1573| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1586| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1586| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLUCONSUPER-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUCONSUPER-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1576| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1576| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLYCEROLMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCEROLMETAB-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1512| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1512| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1577| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1577| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5123| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5123| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1313| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1313| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6387| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6387| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PYRIDNUCSAL-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDNUCSAL-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1578| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1578| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1490| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1490| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1581| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1581| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY3O-4106| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY3O-4106| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|KDOSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|KDOSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7761| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7761| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1582| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1582| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7971| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7971| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1534| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1534| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6952| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6952| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1518| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1518| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7184| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7184| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1584| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1584| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6038| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6038| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PYRIDNUCSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDNUCSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1585| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1585| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-981| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-981| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1495| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1495| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7181| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7181| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7801| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7801| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PYRUVDEHYD-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRUVDEHYD-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5509| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5509| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5350| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5350| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1559| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1559| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ALKANEMONOX-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ALKANEMONOX-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|HOMOSER-METSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HOMOSER-METSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6153| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6153| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1535| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1535| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7206| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7206| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|AST-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|AST-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5340| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5340| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-823| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-823| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-541| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-541| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|THREONINE-DEG2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|THREONINE-DEG2-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5971| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5971| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5436| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5436| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7197| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7197| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|THRDLCTCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|THRDLCTCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1533| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1533| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5437| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5437| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|TRNA-CHARGING-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TRNA-CHARGING-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|LCYSDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|LCYSDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6703| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6703| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1517| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1517| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLYCLEAV-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCLEAV-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GALACTARDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTARDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7446| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7446| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7980| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7980| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ALADEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ALADEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|COA-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|COA-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|HOMOSERSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HOMOSERSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLYOXYLATE-BYPASS| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYOXYLATE-BYPASS| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|SERDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SERDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6163| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6163| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLUTAMINDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUTAMINDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-501| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-501| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-461| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-461| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PROUT-PWY-I| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PROUT-PWY-I| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1275| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1275| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5901| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5901| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ASPARAGINE-DEG1-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ASPARAGINE-DEG1-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|TRYPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TRYPDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6164| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6164| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-522| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-522| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLUTDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUTDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GALACTUROCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTUROCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|HEME-BIOSYNTHESIS-II| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HEME-BIOSYNTHESIS-II| ))\n", + 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"(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1568| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1546| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1546| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|CYANCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|CYANCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|BGALACT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|BGALACT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1501| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1501| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|VALSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|VALSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1466| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1466| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-1269| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-1269| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GALACTITOLCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTITOLCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1481| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1481| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|IDNCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|IDNCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-4261| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-4261| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1182| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1182| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|HISTSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HISTSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|TREDEGLOW-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TREDEGLOW-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-2161| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-2161| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|DTDPRHAMSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DTDPRHAMSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1506| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1506| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1306| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1306| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ACETOACETATE-DEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ACETOACETATE-DEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ENTNER-DOUDOROFF-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ENTNER-DOUDOROFF-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6614| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6614| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|DAPLYSINESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DAPLYSINESYN-PWY| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "variants-of-pathway\n", + "(variants-of-pathway '|RHAMCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|RHAMCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|1CMET2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|1CMET2-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1590| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1590| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7315| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7315| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLYCOGENSYNTH-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCOGENSYNTH-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GALACTCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|DARABCATK12-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DARABCATK12-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1485| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1485| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1338| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1338| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6543| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6543| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|ARABCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ARABCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-661| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-661| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1514| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1514| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7242| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7242| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-43| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-43| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1324| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1324| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GLUCONEO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUCONEO-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|XYLCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|XYLCAT-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-662| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-662| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|SORBDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SORBDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1303| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1303| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1492| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1492| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-301| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-301| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|GALACTMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTMETAB-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-5852| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5852| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PLPSAL-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PLPSAL-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-321| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-321| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6608| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6608| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-4121| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-4121| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1519| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1519| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6961| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6961| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|SALVADEHYPOX-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SALVADEHYPOX-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PYRIDOXSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDOXSYN-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6617| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6617| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1591| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1591| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1497| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1497| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1507| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1507| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6556| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1588| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1588| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PROPIONMET-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PROPIONMET-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1295| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1295| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|RIBOSYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|RIBOSYN2-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1597| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1597| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7195| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1458| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1458| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1321| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1500| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1500| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|HCAMHPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HCAMHPDEG-PWY| ))\n", + "variants-of-pathway\n", + "(variants-of-pathway '|PWY0-1336| )\n", + "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1336| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[],\n", + " [u'|PWY-7195|', u'|PWY-6556|'],\n", + " [u'|PWY0-1597|'],\n", + " [u'|RIBOSYN2-PWY|'],\n", + " [u'|PWY0-1295|', u'|PWY-6556|'],\n", + " [],\n", + " [u'|PWY0-1584|', u'|PWY0-1581|', u'|PWY0-1573|', u'|PWY0-1352|'],\n", + " [],\n", + " [],\n", + " []]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.variants_of_pathway(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1347| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1474| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1474| ))\n", + "pathway-components\n", + "(pathway-components '|PWY-6690| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6690| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1348| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1348| ))\n", + "pathway-components\n", + "(pathway-components '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5162| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1352| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1352| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1505| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1505| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1355| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1355| ))\n", + "pathway-components\n", + "(pathway-components '|2PHENDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|2PHENDEG-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1465| ))\n", + "pathway-components\n", + "(pathway-components '|TRESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|TRESYN-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PANTO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PANTO-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1356| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1356| ))\n", + "pathway-components\n", + "(pathway-components '|ETOH-ACETYLCOA-ANA-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|ETOH-ACETYLCOA-ANA-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1483| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1483| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1573| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1573| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1586| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1586| ))\n", + "pathway-components\n", + "(pathway-components '|GLUCONSUPER-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLUCONSUPER-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1576| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1576| ))\n", + "pathway-components\n", + "(pathway-components '|GLYCEROLMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLYCEROLMETAB-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1512| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1512| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1577| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components 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"(pathway-components '|PWY-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6556| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1588| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1588| ))\n", + "pathway-components\n", + "(pathway-components '|PROPIONMET-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PROPIONMET-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1295| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1295| ))\n", + "pathway-components\n", + "(pathway-components '|RIBOSYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|RIBOSYN2-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1597| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1597| ))\n", + "pathway-components\n", + "(pathway-components '|PWY-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-7195| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1458| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1458| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1321| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1500| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1500| ))\n", + "pathway-components\n", + "(pathway-components '|HCAMHPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|HCAMHPDEG-PWY| ))\n", + "pathway-components\n", + "(pathway-components '|PWY0-1336| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1336| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[[u'|RXN0-5264|', u'|RXN0-5388|']], 1, 2, 2]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|, which is not a super-pathway (i.e., does \n", + "not have any entries in its 'sub‑pathways slot). \n", + "rxn-list\n", + "Optional The list of reactions to use as the starting list of connected \n", + "component clusters. Defaults to (get‑slot‑values pwy 'reaction‑list).\n", + "\n", + "pred-list\n", + "Optional The list of reaction predecessors to iterate from in order to cluster \n", + "the reactions in rxn‑list. Defaults to (get‑slot‑values pwy 'predecessors).\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.pathway_components(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1347| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1474| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1474| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6690| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6690| ))\n", + 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(:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLUTSYNIII-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1568| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1568| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1546| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1546| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|CYANCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|CYANCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|BGALACT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|BGALACT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1501| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1501| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|VALSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|VALSYN-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1466| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1466| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-1269| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-1269| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|GALACTITOLCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTITOLCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1481| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1481| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|IDNCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|IDNCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-4261| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-4261| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1182| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1182| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|HISTSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|HISTSYN-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|TREDEGLOW-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|TREDEGLOW-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-2161| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-2161| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|DTDPRHAMSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|DTDPRHAMSYN-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1506| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1506| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1306| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1306| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|ACETOACETATE-DEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ACETOACETATE-DEG-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|ENTNER-DOUDOROFF-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ENTNER-DOUDOROFF-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6614| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6614| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|DAPLYSINESYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|DAPLYSINESYN-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|RHAMCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|RHAMCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|1CMET2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|1CMET2-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1590| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1590| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-7315| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7315| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|GLYCOGENSYNTH-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLYCOGENSYNTH-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|GALACTCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|DARABCATK12-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|DARABCATK12-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1485| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1485| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1338| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1338| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6543| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6543| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|ARABCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ARABCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-661| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-661| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1514| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1514| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-7242| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7242| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-43| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-43| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1324| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1324| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|GLUCONEO-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLUCONEO-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|XYLCAT-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|XYLCAT-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-662| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-662| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|SORBDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|SORBDEG-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1303| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1303| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1492| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1492| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-301| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-301| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|GALACTMETAB-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTMETAB-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-5852| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5852| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PLPSAL-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PLPSAL-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-321| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-321| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6608| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6608| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-4121| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-4121| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1519| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1519| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6961| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6961| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|SALVADEHYPOX-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|SALVADEHYPOX-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PYRIDOXSYN-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PYRIDOXSYN-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6617| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6617| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1591| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1591| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1497| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1497| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1507| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1507| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-6556| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6556| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1588| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1588| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PROPIONMET-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PROPIONMET-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1295| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1295| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|RIBOSYN2-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|RIBOSYN2-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1597| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1597| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY-7195| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7195| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1458| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1458| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1321| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1321| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1500| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1500| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|HCAMHPDEG-PWY| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|HCAMHPDEG-PWY| ))\n", + "noncontiguous-pathway-p\n", + "(noncontiguous-pathway-p '|PWY0-1336| )\n", + "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1336| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[False, False, False, False, False, True, False, True, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.noncontiguous_pathway_p(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN-15348| '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN-15348| '|PWY0-1347| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| '|LACTALDREDUCT-RXN| '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|LACTALDREDUCT-RXN| '|PWY0-1347| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| '|PFLDEACTIV-RXN| '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|PFLDEACTIV-RXN| '|PWY0-1347| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| '|OHMETPYRKIN-RXN| '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|OHMETPYRKIN-RXN| '|PWY0-1347| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN0-7094| '|PWY0-1347| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN0-7094| '|PWY0-1347| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN-15348| 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'|RXN0-1137| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|OHMETPYRKIN-RXN| '|RXN0-1137| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|OHMETPYRKIN-RXN| '|BADH-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|OHMETPYRKIN-RXN| '|BADH-RXN| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|OHMETPYRKIN-RXN| '|DMKCYT-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|OHMETPYRKIN-RXN| '|DMKCYT-RXN| '|PWY-5162| ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|RXN-15348| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7094| '|RXN-15348| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|LACTALDREDUCT-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7094| '|LACTALDREDUCT-RXN| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|PFLDEACTIV-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7094| '|PFLDEACTIV-RXN| '|PWY-5162| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|OHMETPYRKIN-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7094| '|OHMETPYRKIN-RXN| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|RXN0-7094| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7094| '|RXN0-7094| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7094| '|TRIOSEPISOMERIZATION-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) 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'|RXN0-7094| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7094| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY-5162| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY-5162| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|BADH-RXN| '|PWY-5162| )\n", + "(with-organism (:org-id '|ECOLI|) 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'|RXN0-7298| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7298| '|RXN0-1137| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7298| '|RXN0-1137| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7298| '|BADH-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7298| '|BADH-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-7298| '|DMKCYT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-7298| '|DMKCYT-RXN| '|PWY0-1465| ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN-15348| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN-15348| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|LACTALDREDUCT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|LACTALDREDUCT-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|PFLDEACTIV-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|PFLDEACTIV-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|OHMETPYRKIN-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|OHMETPYRKIN-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7094| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7094| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7298| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7298| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-1137| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-1137| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|BADH-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|BADH-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|DMKCYT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|DMKCYT-RXN| '|PWY0-1465| ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN-15348| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN-15348| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7094| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7094| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|BADH-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|BADH-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|DMKCYT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|DMKCYT-RXN| '|PWY0-1465| ))\n", + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN-15348| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN-15348| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7094| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7094| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7298| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7298| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-1137| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-1137| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|BADH-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|BADH-RXN| '|PWY0-1465| ))\n", + "rxns-adjacent-in-pwy-p\n", + "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|DMKCYT-RXN| '|PWY0-1465| )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|DMKCYT-RXN| '|PWY0-1465| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|DMKCYT-RXN|', u'|RXN-15348|', False],\n", + " [u'|DMKCYT-RXN|', u'|LACTALDREDUCT-RXN|', False],\n", + " [u'|DMKCYT-RXN|', u'|PFLDEACTIV-RXN|', False],\n", + " [u'|DMKCYT-RXN|', u'|OHMETPYRKIN-RXN|', False],\n", + " [u'|DMKCYT-RXN|', u'|RXN0-7094|', False],\n", + " [u'|DMKCYT-RXN|', u'|TRIOSEPISOMERIZATION-RXN|', False],\n", + " [u'|DMKCYT-RXN|', u'|RXN0-7298|', False],\n", + " [u'|DMKCYT-RXN|', u'|RXN0-1137|', False],\n", + " [u'|DMKCYT-RXN|', u'|BADH-RXN|', False],\n", + " [u'|DMKCYT-RXN|', u'|DMKCYT-RXN|', False]]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn1\n", + "An instance of the class |Reactions|. \n", + "rxn2\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True)[0:10]:\n", + " for rxn1 in ecoli.all_rxns(rxn_type = ':all')[0:10]:\n", + " for rxn2 in ecoli.all_rxns(rxn_type = ':all')[0:10]:\n", + " lst.append([rxn1, rxn2, ecoli.rxns_adjacent_in_pwy_p(rxn1 = rxn1, rxn2 = rxn2, pwy = pwy)])\n", + "# lst.append(ecoli.rxns_adjacent_in_pwy_p(rxn1 = u'|RXN0-5264|', rxn2 = u'|RXN0-5388|', pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb b/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb new file mode 100644 index 0000000..a93af8b --- /dev/null +++ b/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb @@ -0,0 +1,1277 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[u'|META|', u'|ECOLI|']\n", + "class-name-p\n", + "(class-name-p \"proteins\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"proteins\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Proteins| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Proteins| ))\n", + "get-class\n", + "(get-class |Proteins| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Proteins| ))\n", + "all-protein-complexes\n", + "(all-protein-complexes :filter :all)\n", + "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "complexes = ecoli.all_protein_complexes()[0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "monomers-of-protein\n", + "(monomers-of-protein '|CPLX0-7660| :coefficients? t :unmodify? t)\n", + "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|CPLX0-7660| :coefficients? t :unmodify? t))\n", + "monomers-of-protein\n", + "(monomers-of-protein '|CPLX0-8247| :coefficients? t :unmodify? t)\n", + "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|CPLX0-8247| :coefficients? t :unmodify? t))\n", + "[[[u'|G6106-MONOMER|'], [4]], [[u'|URAA-MONOMER|'], [2]]]\n", + "monomers-of-protein\n", + "(monomers-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|OPPC-MONOMER| ))\n", + "monomers-of-protein\n", + "(monomers-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|YHBN-MONOMER| ))\n", + "[[[u'|OPPC-MONOMER|'], [1]], [[u'|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "coefficients?\n", + "Keyword, Optional If true, then the second return value of the function will be \n", + "a list of monomer coefficients. Defaults to true. \n", + "unmodify?\n", + "Keyword, Optional If true, obtain the monomers of the unmodified form of p.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein, coefficients = True, unmodify = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "base-components-of-protein\n", + "(base-components-of-protein '|CPLX0-7660| :exclude-small-molecules? t)\n", + "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|CPLX0-7660| :exclude-small-molecules? t))\n", + "base-components-of-protein\n", + "(base-components-of-protein '|CPLX0-8247| :exclude-small-molecules? t)\n", + "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|CPLX0-8247| :exclude-small-molecules? t))\n", + "[[[u'|G6106-MONOMER|'], [4]], [[u'|URAA-MONOMER|'], [2]]]\n", + "base-components-of-protein\n", + "(base-components-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|OPPC-MONOMER| ))\n", + "base-components-of-protein\n", + "(base-components-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|YHBN-MONOMER| ))\n", + "[[[u'|OPPC-MONOMER|'], [1]], [[u'|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "exclude-small-molecules?\n", + "Keyword, Optional If nil, then small molecule components are also returned. \n", + "Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein, exclude_small_molecules = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "containers-of\n", + "(containers-of '|CPLX0-7660| t )\n", + "(with-organism (:org-id '|ECOLI|) (containers-of '|CPLX0-7660| t ))\n", + "containers-of\n", + "(containers-of '|CPLX0-8247| t )\n", + "(with-organism (:org-id '|ECOLI|) (containers-of '|CPLX0-8247| t ))\n", + "[[], []]\n", + "containers-of\n", + "(containers-of '|OPPC-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (containers-of '|OPPC-MONOMER| nil ))\n", + "containers-of\n", + "(containers-of '|YHBN-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (containers-of '|YHBN-MONOMER| nil ))\n", + "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.containers_of(protein = protein, exclude_self = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "protein-or-rna-containers-of\n", + "(protein-or-rna-containers-of '|CPLX0-7660| nil )\n", + "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|CPLX0-7660| nil ))\n", + "protein-or-rna-containers-of\n", + "(protein-or-rna-containers-of '|CPLX0-8247| nil )\n", + "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|CPLX0-8247| nil ))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "protein-or-rna-containers-of\n", + "(protein-or-rna-containers-of '|OPPC-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|OPPC-MONOMER| nil ))\n", + "protein-or-rna-containers-of\n", + "(protein-or-rna-containers-of '|YHBN-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|YHBN-MONOMER| nil ))\n", + "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "homomultimeric-containers-of\n", + "(homomultimeric-containers-of '|CPLX0-7660| nil )\n", + "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|CPLX0-7660| nil ))\n", + "homomultimeric-containers-of\n", + "(homomultimeric-containers-of '|CPLX0-8247| nil )\n", + "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|CPLX0-8247| nil ))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "homomultimeric-containers-of\n", + "(homomultimeric-containers-of '|OPPC-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|OPPC-MONOMER| nil ))\n", + "homomultimeric-containers-of\n", + "(homomultimeric-containers-of '|YHBN-MONOMER| nil )\n", + "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|YHBN-MONOMER| nil ))\n", + "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "polypeptide-or-homomultimer-p\n", + "(polypeptide-or-homomultimer-p '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|CPLX0-7660| ))\n", + "polypeptide-or-homomultimer-p\n", + "(polypeptide-or-homomultimer-p '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|CPLX0-8247| ))\n", + "[True, True]\n", + "polypeptide-or-homomultimer-p\n", + "(polypeptide-or-homomultimer-p '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|OPPC-MONOMER| ))\n", + "polypeptide-or-homomultimer-p\n", + "(polypeptide-or-homomultimer-p '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|YHBN-MONOMER| ))\n", + "[True, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "unmodified-form\n", + "(unmodified-form '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-form '|CPLX0-7660| ))\n", + "unmodified-form\n", + "(unmodified-form '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-form '|CPLX0-8247| ))\n", + "[u'|CPLX0-7660|', u'|CPLX0-8247|']\n", + "unmodified-form\n", + "(unmodified-form '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-form '|OPPC-MONOMER| ))\n", + "unmodified-form\n", + "(unmodified-form '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-form '|YHBN-MONOMER| ))\n", + "[u'|OPPC-MONOMER|', u'|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "unmodified-or-unbound-form\n", + "(unmodified-or-unbound-form '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|CPLX0-7660| ))\n", + "unmodified-or-unbound-form\n", + "(unmodified-or-unbound-form '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|CPLX0-8247| ))\n", + "[u'|CPLX0-7660|', u'|CPLX0-8247|']\n", + "unmodified-or-unbound-form\n", + "(unmodified-or-unbound-form '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|OPPC-MONOMER| ))\n", + "unmodified-or-unbound-form\n", + "(unmodified-or-unbound-form '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|YHBN-MONOMER| ))\n", + "[u'|OPPC-MONOMER|', u'|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reduce-modified-proteins\n", + "(reduce-modified-proteins '(|CPLX0-7660|) :debind? t)\n", + "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|CPLX0-7660|) :debind? t))\n", + "reduce-modified-proteins\n", + "(reduce-modified-proteins '(|CPLX0-8247|) :debind? t)\n", + "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|CPLX0-8247|) :debind? t))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "reduce-modified-proteins\n", + "(reduce-modified-proteins '(|OPPC-MONOMER|) )\n", + "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|OPPC-MONOMER|) ))\n", + "reduce-modified-proteins\n", + "(reduce-modified-proteins '(|YHBN-MONOMER|) )\n", + "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|YHBN-MONOMER|) ))\n", + "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "prots\n", + "A list of instances of the class |Proteins|. \n", + "debind?\n", + "Keyword, Optional When non-nil, the proteins are further simplified by obtaining \n", + "the unbound form of the protein, if it is bound to a small molecule. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein], debind = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein]))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-direct-forms-of-protein\n", + "(all-direct-forms-of-protein '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|CPLX0-7660| ))\n", + "all-direct-forms-of-protein\n", + "(all-direct-forms-of-protein '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|CPLX0-8247| ))\n", + "[[u'|G6106-MONOMER|', u'|CPLX0-7660|'], [u'|URAA-MONOMER|', u'|CPLX0-8247|']]\n", + "all-direct-forms-of-protein\n", + "(all-direct-forms-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|OPPC-MONOMER| ))\n", + "all-direct-forms-of-protein\n", + "(all-direct-forms-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|YHBN-MONOMER| ))\n", + "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-forms-of-protein\n", + "(all-forms-of-protein '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|CPLX0-7660| ))\n", + "all-forms-of-protein\n", + "(all-forms-of-protein '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|CPLX0-8247| ))\n", + "[[u'|G6106-MONOMER|', u'|CPLX0-7660|'], [u'|URAA-MONOMER|', u'|CPLX0-8247|']]\n", + "all-forms-of-protein\n", + "(all-forms-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|OPPC-MONOMER| ))\n", + "all-forms-of-protein\n", + "(all-forms-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|YHBN-MONOMER| ))\n", + "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "modified-forms\n", + "(modified-forms '|CPLX0-7660| t t )\n", + "(with-organism (:org-id '|ECOLI|) (modified-forms '|CPLX0-7660| t t ))\n", + "modified-forms\n", + "(modified-forms '|CPLX0-8247| t t )\n", + "(with-organism (:org-id '|ECOLI|) (modified-forms '|CPLX0-8247| t t ))\n", + "[[], []]\n", + "modified-forms\n", + "(modified-forms '|OPPC-MONOMER| nil nil )\n", + "(with-organism (:org-id '|ECOLI|) (modified-forms '|OPPC-MONOMER| nil nil ))\n", + "modified-forms\n", + "(modified-forms '|YHBN-MONOMER| nil nil )\n", + "(with-organism (:org-id '|ECOLI|) (modified-forms '|YHBN-MONOMER| nil nil ))\n", + "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_forms(protein = protein, all_variants = True, exclude_self= True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "modified-and-unmodified-forms\n", + "(modified-and-unmodified-forms '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|CPLX0-7660| ))\n", + "modified-and-unmodified-forms\n", + "(modified-and-unmodified-forms '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|CPLX0-8247| ))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "modified-and-unmodified-forms\n", + "(modified-and-unmodified-forms '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|OPPC-MONOMER| ))\n", + "modified-and-unmodified-forms\n", + "(modified-and-unmodified-forms '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|YHBN-MONOMER| ))\n", + "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "modified-containers\n", + "(modified-containers '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-containers '|CPLX0-7660| ))\n", + "modified-containers\n", + "(modified-containers '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-containers '|CPLX0-8247| ))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "modified-containers\n", + "(modified-containers '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-containers '|OPPC-MONOMER| ))\n", + "modified-containers\n", + "(modified-containers '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (modified-containers '|YHBN-MONOMER| ))\n", + "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "top-containers\n", + "(top-containers '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (top-containers '|CPLX0-7660| ))\n", + "top-containers\n", + "(top-containers '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (top-containers '|CPLX0-8247| ))\n", + "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", + "top-containers\n", + "(top-containers '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (top-containers '|OPPC-MONOMER| ))\n", + "top-containers\n", + "(top-containers '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (top-containers '|YHBN-MONOMER| ))\n", + "[[u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "small-molecule-cplxes-of-prot\n", + "(small-molecule-cplxes-of-prot '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|CPLX0-7660| ))\n", + "small-molecule-cplxes-of-prot\n", + "(small-molecule-cplxes-of-prot '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|CPLX0-8247| ))\n", + "[[], []]\n", + "small-molecule-cplxes-of-prot\n", + "(small-molecule-cplxes-of-prot '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|OPPC-MONOMER| ))\n", + "small-molecule-cplxes-of-prot\n", + "(small-molecule-cplxes-of-prot '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-of-protein\n", + "(genes-of-protein '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|CPLX0-7660| ))\n", + "genes-of-protein\n", + "(genes-of-protein '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|CPLX0-8247| ))\n", + "[[u'|G6106|'], [u'|EG12129|']]\n", + "genes-of-protein\n", + "(genes-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|OPPC-MONOMER| ))\n", + "genes-of-protein\n", + "(genes-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|YHBN-MONOMER| ))\n", + "[[u'|EG10676|'], [u'|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-of-proteins\n", + "(genes-of-proteins '(|CPLX0-7660|) )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|CPLX0-7660|) ))\n", + "genes-of-proteins\n", + "(genes-of-proteins '(|CPLX0-8247|) )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|CPLX0-8247|) ))\n", + "[[u'|G6106|'], [u'|EG12129|']]\n", + "genes-of-proteins\n", + "(genes-of-proteins '(|OPPC-MONOMER|) )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|OPPC-MONOMER|) ))\n", + "genes-of-proteins\n", + "(genes-of-proteins '(|YHBN-MONOMER|) )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|YHBN-MONOMER|) ))\n", + "[[u'|EG10676|'], [u'|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reactions-of-enzyme\n", + "(reactions-of-enzyme '|CPLX0-7660| :include-subreactions? t)\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|CPLX0-7660| :include-subreactions? t))\n", + "reactions-of-enzyme\n", + "(reactions-of-enzyme '|CPLX0-8247| :include-subreactions? t)\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|CPLX0-8247| :include-subreactions? t))\n", + "[[u'|RXN0-4301|'], [u'|TRANS-RXN-132|']]\n", + "reactions-of-enzyme\n", + "(reactions-of-enzyme '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|OPPC-MONOMER| ))\n", + "reactions-of-enzyme\n", + "(reactions-of-enzyme '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "kb\n", + "Keyword, Optional The KB object of the KB in which to find the associated \n", + "reactions. Defaults to the current PGDB. \n", + "include-specific-forms?\n", + "Keyword, Optional When true, specific forms of associated generic reactions are \n", + "also returned. Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein, include_subreactions = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "species-of-protein\n", + "(species-of-protein '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (species-of-protein '|CPLX0-7660| ))\n", + "species-of-protein\n", + "(species-of-protein '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (species-of-protein '|CPLX0-8247| ))\n", + "[[u'|ECOLI|'], [u'|ECOLI|']]\n", + "species-of-protein\n", + "(species-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (species-of-protein '|OPPC-MONOMER| ))\n", + "species-of-protein\n", + "(species-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (species-of-protein '|YHBN-MONOMER| ))\n", + "[[u'|ECOLI|'], [u'|ECOLI|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzyme-p\n", + "(enzyme-p '|CPLX0-7660| :any )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-p '|CPLX0-7660| :any ))\n", + "enzyme-p\n", + "(enzyme-p '|CPLX0-8247| :any )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-p '|CPLX0-8247| :any ))\n", + "[True, True]\n", + "enzyme-p\n", + "(enzyme-p '|OPPC-MONOMER| :non-transport-non-pathway )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-p '|OPPC-MONOMER| :non-transport-non-pathway ))\n", + "enzyme-p\n", + "(enzyme-p '|YHBN-MONOMER| :non-transport-non-pathway )\n", + "(with-organism (:org-id '|ECOLI|) (enzyme-p '|YHBN-MONOMER| :non-transport-non-pathway ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Optional Can take on one of the following values to select more precisely what \n", + "is meant by an “enzyme”:\n", + "\n", + ":any\n", + "Any protein that catalyzes a reaction is considered an enzyme. \n", + ":chemical-change\n", + "If the reactants and products of the catalyzed reactin differ, and not just by \n", + "their cellular location, then the protein is considered an enzyme. \n", + ":small-molecule\n", + "If the reactants of the catalyzed reaction differ and are small molecules, then \n", + "the protein is considered an enzyme. \n", + ":transport\n", + "If the protein catalyzes a transport reaction. \n", + ":non-transport\n", + "If the protein only catalyzes non-transport reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'any'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'non-transport-non-pathway'))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "leader-peptide?\n", + "(leader-peptide? '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (leader-peptide? '|CPLX0-7660| ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for protein in complexes:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "protein-p\n", + "(protein-p '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (protein-p '|CPLX0-7660| ))\n", + "protein-p\n", + "(protein-p '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (protein-p '|CPLX0-8247| ))\n", + "[u'|Proteins|', u'|Proteins|']\n", + "protein-p\n", + "(protein-p '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (protein-p '|OPPC-MONOMER| ))\n", + "protein-p\n", + "(protein-p '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (protein-p '|YHBN-MONOMER| ))\n", + "[u'|Proteins|', u'|Proteins|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "complex-p\n", + "(complex-p '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (complex-p '|CPLX0-7660| ))\n", + "complex-p\n", + "(complex-p '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (complex-p '|CPLX0-8247| ))\n", + "[u'|Protein-Complexes|', u'|Protein-Complexes|']\n", + "complex-p\n", + "(complex-p '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (complex-p '|OPPC-MONOMER| ))\n", + "complex-p\n", + "(complex-p '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (complex-p '|YHBN-MONOMER| ))\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reactions-of-protein\n", + "(reactions-of-protein '|CPLX0-7660| nil t )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|CPLX0-7660| nil t ))\n", + "reactions-of-protein\n", + "(reactions-of-protein '|CPLX0-8247| nil t )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|CPLX0-8247| nil t ))\n", + "[[u'|RXN0-4301|'], [u'|TRANS-RXN-132|']]\n", + "reactions-of-protein\n", + "(reactions-of-protein '|OPPC-MONOMER| t nil )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|OPPC-MONOMER| t nil ))\n", + "reactions-of-protein\n", + "(reactions-of-protein '|YHBN-MONOMER| t nil )\n", + "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|YHBN-MONOMER| t nil ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "check-protein-components?\n", + "Optional If true, check all components of this protein for catalyzed reactions. \n", + "Defaults to true. \n", + "check-protein-containers?\n", + "Optional If true, check the containers and modified forms of the protein for \n", + "catalyzed reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_containers = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_components = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "protein-in-compartment-p\n", + "(protein-in-compartment-p '|CPLX0-7660| 'CCO-CYTOSOL )\n", + "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|CPLX0-7660| 'CCO-CYTOSOL ))\n", + "protein-in-compartment-p\n", + "(protein-in-compartment-p '|CPLX0-8247| 'CCO-CYTOSOL )\n", + "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|CPLX0-8247| 'CCO-CYTOSOL ))\n", + "[False, False]\n", + "protein-in-compartment-p\n", + "(protein-in-compartment-p '|OPPC-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) )\n", + "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|OPPC-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) ))\n", + "protein-in-compartment-p\n", + "(protein-in-compartment-p '|YHBN-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) )\n", + "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|YHBN-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) ))\n", + "[u'|CCI-CYTOSOL-GN|', False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = 'CCO-CYTOSOL'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = ['CCO-CYTOSOL', 'CCO-MEMBRANE']))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-transporters-across\n", + "(all-transporters-across :membranes :all)\n", + "(with-organism (:org-id '|ECOLI|) (all-transporters-across :membranes :all))\n", + "[u'|MTR-MONOMER|', u'|G7942-MONOMER|', u'|NANT-MONOMER|', u'|B1006-MONOMER|', u'|YDHE-MONOMER|', u'|YDEA-MONOMER|', u'|PITA-MONOMER|', u'|YEIM-MONOMER|', u'|BCR-MONOMER|', u'|YGFO-MONOMER|']\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "membranes\n", + "Keyword Either :all or a list of instances of the class. Defaults to :all \n", + "'CCO‑MEMBRANE. \n", + "method\n", + "Either :location or :reaction‑compartments. :location will check the 'locations \n", + "slot, while :reaction‑compartments will examine the compartments of reaction \n", + "substrates. Default value is :location. \n", + "\"\"\"\n", + "\n", + "lst = ecoli.all_transporters_across(membranes = 'all')\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "autocatalytic-reactions-of-enzyme\n", + "(autocatalytic-reactions-of-enzyme '|CPLX0-7660| )\n", + "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|CPLX0-7660| ))\n", + "autocatalytic-reactions-of-enzyme\n", + "(autocatalytic-reactions-of-enzyme '|CPLX0-8247| )\n", + "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|CPLX0-8247| ))\n", + "[[], []]\n", + "autocatalytic-reactions-of-enzyme\n", + "(autocatalytic-reactions-of-enzyme '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|OPPC-MONOMER| ))\n", + "autocatalytic-reactions-of-enzyme\n", + "(autocatalytic-reactions-of-enzyme '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Reactions.ipynb b/examples/ptools API - Operations on Reactions.ipynb new file mode 100644 index 0000000..9300ed3 --- /dev/null +++ b/examples/ptools API - Operations on Reactions.ipynb @@ -0,0 +1,122770 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[u'|META|', u'|ECOLI|']\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-15348| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|LACTALDREDUCT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PFLDEACTIV-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|OHMETPYRKIN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7094| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7298| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1137| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|BADH-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DMKCYT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5061| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|FES-OX-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16000| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6505| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PEPCARBOX-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2601| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MENCYT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7003| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CARNDETRU-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14505| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ADPREDUCT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5118| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CHEBTAPD-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16650| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MALATE-DEH-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DEPHOSICITDEHASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|GDPREDUCT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXNMETA-12672| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|MYRISTOYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MYRISTOYLACYLTRAN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|COBINPGUANYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|COBINPGUANYLYLTRANS-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PROTEIN-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PROTEIN-KINASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5183| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5183| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ADENYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ADENYL-KIN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-10658| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16910| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-12473| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-12473| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-2942| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2942| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-16381| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16381| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|YIAE2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|YIAE2-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-17355| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17355| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|D-PPENTOMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|D-PPENTOMUT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14570| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14570| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-19340| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-19340| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5216| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5216| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-5741| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-5741| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-17393| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17393| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|METBALT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|METBALT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-9533| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-9533| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PROLINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PROLINE--TRNA-LIGASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-9660| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-9660| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DEOXYADENPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DEOXYADENPHOSPHOR-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|SPONTPRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|SPONTPRO-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-1144| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1144| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5292| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5292| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5098| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5098| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-17701| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17701| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ALCOHOL-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ALCOHOL-DEHYDROG-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-6435| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6435| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-6547| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6547| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DIAMACTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DIAMACTRANS-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-3241| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-3241| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-745| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-745| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5387| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5387| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-17783| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17783| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14883| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14883| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|1.3.1.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|1.3.1.9-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|R170-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|R170-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|2.7.3.9-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|2.7.3.9-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DLACTDEHYDROGNAD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DLACTDEHYDROGNAD-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|N-ACETYLTRANSFER-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|N-ACETYLTRANSFER-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ARCB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ARCB-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-5435| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5435| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|CHEBTSRD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CHEBTSRD-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-17799| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17799| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|TAGAKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TAGAKIN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ENOYL-ACP-REDUCT-NADPH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ENOYL-ACP-REDUCT-NADPH-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RIBOSYLHOMOCYSTEINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RIBOSYLHOMOCYSTEINASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|NARLX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|NARLX-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DUTP-PYROP-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DUTP-PYROP-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|AMINOBUTDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|AMINOBUTDEHYDROG-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|PYRUFLAVREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PYRUFLAVREDUCT-RXN| ))\n", + "genes-of-reaction\n", + 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+ "genes-of-reaction\n", + "(genes-of-reaction '|ADENPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ADENPRIBOSYLTRAN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-2941| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2941| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|5-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|5-NUCLEOTID-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14569| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14569| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MERCAPYSTRANS-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1401| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|SPERMIDINESYN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7049| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14255| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1130| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-3221| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|UBIQUINOL-OX-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14882| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|KDO-8PPHOSPHAT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DMK-FE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DSBDC-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TAGAALDOL-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7230| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MEN-FE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|AMINEPHEN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7048| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-384| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7096| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-15139| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-5068| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2022| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7310| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|THREOSPON-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CYTC-RED-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ARGSUCCINSYN-RXN| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14394| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-3141| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-4342| ))\n", + "genes-of-reaction\n", + "(genes-of-reaction '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|G6350|'],\n", + " [u'|EG10754|'],\n", + " [],\n", + " [],\n", + " [],\n", + " [u'|EG10068|'],\n", + " [u'|EG10278|', u'|G7213|'],\n", + " [],\n", + " [u'|G7590|'],\n", + " []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.genes_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-15348| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|LACTALDREDUCT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PFLDEACTIV-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|OHMETPYRKIN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7094| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7298| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1137| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|BADH-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DMKCYT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5061| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|FES-OX-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-16000| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-6505| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PEPCARBOX-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2601| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MENCYT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7003| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|CARNDETRU-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14505| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ADPREDUCT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5118| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|CHEBTAPD-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-16650| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MALATE-DEH-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DEPHOSICITDEHASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|GDPREDUCT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXNMETA-12672| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|MYRISTOYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MYRISTOYLACYLTRAN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|COBINPGUANYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|COBINPGUANYLYLTRANS-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PROTEIN-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PROTEIN-KINASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-5183| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5183| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ADENYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ADENYL-KIN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-10658| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-16910| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-12473| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-12473| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-2942| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2942| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-16381| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-16381| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|YIAE2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|YIAE2-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-17355| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-17355| ))\n", + "substrates-of-reaction\n", + 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(:org-id '|ECOLI|) (substrates-of-reaction '|PRTRANS-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14112| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14112| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DETHIOBIOTIN-SYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DETHIOBIOTIN-SYN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|HYPOXANPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|HYPOXANPRIBOSYLTRAN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-8506| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-8506| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-5311| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5311| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7122| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7122| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-17775| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-17775| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|5-FORMYL-THF-CYCLO-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|5-FORMYL-THF-CYCLO-LIGASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-13854| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-13854| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|PYRUVATEDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PYRUVATEDECARB-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-1382| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1382| ))\n", + "substrates-of-reaction\n", + 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"substrates-of-reaction\n", + "(substrates-of-reaction '|3.4.24.55-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|3.4.24.55-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-5515| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5515| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14393| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14393| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-17905| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-17905| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|LACTALDDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|LACTALDDEHYDROG-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-9311| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-9311| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-10016| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-10016| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7291| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7291| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ERYTH4PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ERYTH4PDEHYDROG-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ACNEULY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ACNEULY-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14113| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14113| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-6389| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-6389| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-2584| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2584| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14503| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14503| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|IGPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|IGPSYN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|LYXK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|LYXK-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXNMETA-12671| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXNMETA-12671| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7139| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7139| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ADENPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ADENPRIBOSYLTRAN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-2941| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2941| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|5-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|5-NUCLEOTID-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14569| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14569| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MERCAPYSTRANS-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1401| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|SPERMIDINESYN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7049| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14255| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1130| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-3221| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|UBIQUINOL-OX-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14882| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|KDO-8PPHOSPHAT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DMK-FE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DSBDC-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|TAGAALDOL-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7230| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MEN-FE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|AMINEPHEN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7048| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-384| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7096| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-15139| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-5068| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2022| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7310| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|THREOSPON-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|CYTC-RED-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ARGSUCCINSYN-RXN| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14394| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-3141| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-4342| ))\n", + "substrates-of-reaction\n", + "(substrates-of-reaction '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|NICOTINATE_NUCLEOTIDE|',\n", + " u'|ATP|',\n", + " u'|PROTON|',\n", + " u'|PPI|',\n", + " u'|DEAMIDO-NAD|'],\n", + " [u'|ACETALD|', u'|PYRUVATE|', u'|PROTON|', u'|ACETOIN|', u'|CARBON-DIOXIDE|'],\n", + " [u'|Protein-Red-Disulfides|',\n", + " u'|MONOMER0-4152|',\n", + " u'|MONOMER0-4438|',\n", + " u'|Protein-Ox-Disulfides|'],\n", + " [u'|PROTON|', u'|AMINO-OXOBUT|', u'|AMINO-ACETONE|', u'|CARBON-DIOXIDE|'],\n", + " [u'|Cytochromes-B-Reduced|', u'|Cytochromes-B|', u'|Reduced-Cytochromes-o|'],\n", + " [u'|ATP|',\n", + " u'|L-CITRULLINE|',\n", + " u'|L-ASPARTATE|',\n", + " u'|PROTON|',\n", + " u'|L-ARGININO-SUCCINATE|',\n", + " u'|PPI|',\n", + " u'|AMP|'],\n", + " [u'|ACETYL-COA|', u'|CPD-7221|', u'|CPD-15244|', u'|CO-A|'],\n", + " [u'|MONOMER0-1641|', u'|TORR-CPLX|', u'|CPLX0-2821|'],\n", + " [u'|ATP|',\n", + " u'|D-BETA-D-HEPTOSE-1-P|',\n", + " u'|PROTON|',\n", + " u'|ADP-D-GLYCERO-D-MANNO-HEPTOSE|',\n", + " u'|PPI|'],\n", + " [u'|DSBD-MONOMER|', u'|CPLX0-8004|', u'|DSBG-MONOMER|', u'|DSBDOXI-MONOMER|']]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.substrates_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-15348| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15348| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|LACTALDREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|LACTALDREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|PFLDEACTIV-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PFLDEACTIV-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|OHMETPYRKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|OHMETPYRKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7094| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + 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'|3-OXOACYL-ACP-SYNTH-BASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5239| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5239| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|3.1.13.3-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.1.13.3-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6990| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6990| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", 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:experimental-only? nil :local-only-p nil)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.4.17.8-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7022| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7022| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-9556| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-9556| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7284| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7284| :species 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'|ECOLI|) (enzymes-of-reaction '|DNA-DIRECTED-DNA-POLYMERASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-9528| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-9528| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|THIKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THIKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-9657| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-9657| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ARABISOM-RXN| 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"enzymes-of-reaction\n", + "(enzymes-of-reaction '|RIBULPEPIM-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RIBULPEPIM-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|2.3.1.41-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|2.3.1.41-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-549| :species '|ECOLI| :experimental-only? nil :local-only-p 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'|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-11277| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-11277| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5264| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5264| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|CHORISMATEMUT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CHORISMATEMUT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-273| :species '|ECOLI| :experimental-only? nil :local-only-p 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nil :local-only-p nil)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-1603| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-500| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-500| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-19776| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-19776| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14812| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14812| :species '|ECOLI| 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'|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|THREDEHYD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THREDEHYD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ACETOLACTSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ACETOLACTSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-578| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) 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"stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|CYTIDEAM2-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CYTIDEAM2-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|AGMATIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|AGMATIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7124| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7124| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|3.2.2.21-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) 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:species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-205A| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-205A| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|4.2.1.99-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|4.2.1.99-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6446| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6446| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-262| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-262| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6452| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6452| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-4022| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-4022| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-290| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-290| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-1081| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-1081| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-18258| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-18258| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|R601-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|R601-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-11475| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-11475| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-15296| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15296| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-313| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-313| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14161| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14161| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|GALACTARDEHYDRA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|GALACTARDEHYDRA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6502| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6502| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|NUCLEOSIDE-DIPHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|NUCLEOSIDE-DIPHOSPHATASE-RXN| :species '|ECOLI| 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nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7222| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7222| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7272| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7272| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-12107| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-12107| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ABC-24-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction 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:experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-8461| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-8461| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-17755| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-17755| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-1381| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-1381| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-16688| :species '|ECOLI| 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"enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-108| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-108| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-15312| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15312| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|N-ACETYLGLUCOSAMINE-KINASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|N-ACETYLGLUCOSAMINE-KINASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ASNSYNB-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism 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:experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-11326| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-11326| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7206| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7206| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|PGPPHOSPHA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PGPPHOSPHA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|COBINAMIDEKIN-RXN| 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"(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7246| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|2.1.1.34-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|2.1.1.34-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ACONITATEDEHYDR-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ACONITATEDEHYDR-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ABC-4-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ABC-4-RXN| :species '|ECOLI| 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:experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|DMK-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DMK-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-348| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-348| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5455| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5455| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-15123| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism 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:experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-364| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RIBOSYLPYRIMIDINE-NUCLEOSIDASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RIBOSYLPYRIMIDINE-NUCLEOSIDASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|NAG6PDEACET-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|NAG6PDEACET-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-56| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + 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(enzymes-of-reaction '|GLUTATHIONE-PEROXIDASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|P-PANTOCYSLIG-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|P-PANTOCYSLIG-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-106B| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-106B| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14379| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14379| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction 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nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7283| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7283| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|GLYCINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|GLYCINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5266| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5266| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6973| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id 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nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|3.1.13.1-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.1.13.1-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5330| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5330| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-6081| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-6081| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-16420| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction 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'|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|3.4.15.5-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.4.15.5-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-13519| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-13519| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-8654| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction 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:local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-16| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-16| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-11838| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-11838| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|THYMIDYLATE-5-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THYMIDYLATE-5-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-478| 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:experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-16996| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-16996| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-168| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-168| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-8348| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-8348| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|COBALAMIN5PSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + 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:local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-279| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-279| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-18703| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-18703| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-519| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-519| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14525| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) 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:species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5375| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5375| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-6523| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6523| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-579| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-579| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ALANINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ALANINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|2-METHYLCITRATE-SYNTHASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|2-METHYLCITRATE-SYNTHASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-601| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-601| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-313| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) 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nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|R15-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|R15-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|GLUCONOKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|GLUCONOKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN-108H| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-108H| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|SULFITE-REDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) 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'|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-274| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-16457| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-16457| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-13248| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-13248| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TRANS-RXN0-445| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-445| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|URA-PHOSPH-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|URA-PHOSPH-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-10856| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-10856| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|H2NEOPTERINALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|H2NEOPTERINALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-12| :species '|ECOLI| 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:local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-5146| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5146| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|FGAMSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|FGAMSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|3.4.21.102-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.4.21.102-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7191| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id 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nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-12195| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-12195| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-4121| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-4121| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ABC-25-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ABC-25-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-19362| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction 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:experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14882| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14882| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|KDO-8PPHOSPHAT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|KDO-8PPHOSPHAT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|DMK-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DMK-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|DSBDC-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DSBDC-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|TAGAALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TAGAALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7230| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7230| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|MEN-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|MEN-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|AMINEPHEN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|AMINEPHEN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7048| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7048| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-384| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-384| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ACETATE--COA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ACETATE--COA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7096| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7096| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-15139| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15139| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-5068| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-5068| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|NICONUCADENYLYLTRAN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|NICONUCADENYLYLTRAN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-2022| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-2022| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-7310| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7310| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|THREOSPON-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THREOSPON-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|CYTC-RED-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CYTC-RED-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|ARGSUCCINSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ARGSUCCINSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN-14394| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14394| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-3141| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-3141| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|RXN0-4342| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-4342| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", + "enzymes-of-reaction\n", + "(enzymes-of-reaction '|DSBD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", + "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DSBD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|NICONUCADENYLYLTRAN-MONOMER|'],\n", + " [u'|PYRUVOXID-CPLX|'],\n", + " [],\n", + " [],\n", + " [],\n", + " [u'|CPLX0-238|'],\n", + " [u'|G7213-MONOMER|', u'|FADA-CPLX|'],\n", + " [],\n", + " [u'|CPLX0-3661|'],\n", + " []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. Default value \n", + "is nil. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "local-only-p\n", + "Keyword, Optional When true, only return enzymes that catalyze the specific form \n", + "of the reaction, as opposed to enzymes that are known to catalyze a more general \n", + "form (i.e., class) of the reaction. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.enzymes_of_reaction(rxn = rxn, species = u'|ECOLI|', \n", + " experimental_only = False, local_only_p = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-15348| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|LACTALDREDUCT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PFLDEACTIV-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|OHMETPYRKIN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7094| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|TRIOSEPISOMERIZATION-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7298| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-1137| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|BADH-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DMKCYT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5061| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|FES-OX-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16000| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-6505| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PEPCARBOX-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2601| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MENCYT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7003| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CARNDETRU-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14505| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ADPREDUCT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5118| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CHEBTAPD-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16650| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MALATE-DEH-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DEPHOSICITDEHASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|GDPREDUCT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXNMETA-12672| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|MYRISTOYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MYRISTOYLACYLTRAN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|COBINPGUANYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|COBINPGUANYLYLTRANS-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|PROTEIN-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PROTEIN-KINASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-5183| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5183| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ADENYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ADENYL-KIN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-10658| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16910| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-12473| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-12473| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2942| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2942| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-16381| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16381| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|YIAE2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|YIAE2-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-17355| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-17355| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|D-PPENTOMUT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|D-PPENTOMUT-RXN| ))\n", + "reaction-reactants-and-products\n", + 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"(reaction-reactants-and-products '|DIHYDROFOLATESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DIHYDROFOLATESYNTH-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14251| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14251| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|HISTAMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|HISTAMINOTRANS-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-5408| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5408| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|KDGALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|KDGALDOL-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-17791| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-17791| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7229| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7229| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7078| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7078| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RHAMNULPALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RHAMNULPALDOL-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ACETALD-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACETALD-DEHYDROG-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DTDPDEHYDRHAMEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DTDPDEHYDRHAMEPIM-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2001| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2001| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|3.4.24.55-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|3.4.24.55-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-5515| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5515| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14393| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14393| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-17905| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-17905| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|LACTALDDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|LACTALDDEHYDROG-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-9311| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-9311| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-10016| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-10016| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7291| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7291| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ERYTH4PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ERYTH4PDEHYDROG-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ACNEULY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACNEULY-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14113| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14113| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-6389| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-6389| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2584| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2584| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14503| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14503| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|IGPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|IGPSYN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|LYXK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|LYXK-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXNMETA-12671| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXNMETA-12671| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7139| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7139| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ADENPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ADENPRIBOSYLTRAN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2941| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2941| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|5-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|5-NUCLEOTID-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14569| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14569| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MERCAPYSTRANS-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-1401| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|SPERMIDINESYN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7049| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14255| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-1130| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-3221| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|UBIQUINOL-OX-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14882| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|KDO-8PPHOSPHAT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DMK-FE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DSBDC-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|TAGAALDOL-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7230| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MEN-FE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|AMINEPHEN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7048| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-384| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACETATE--COA-LIGASE-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7096| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-15139| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-5068| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|NICONUCADENYLYLTRAN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2022| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7310| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|THREOSPON-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CYTC-RED-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ARGSUCCINSYN-RXN| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14394| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-3141| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-4342| ))\n", + "reaction-reactants-and-products\n", + "(reaction-reactants-and-products '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[[u'|PROTON|', u'|ATP|', u'|NICOTINATE_NUCLEOTIDE|'],\n", + " [u'|PPI|', u'|DEAMIDO-NAD|']],\n", + " [[u'|PROTON|', u'|PYRUVATE|', u'|ACETALD|'],\n", + " [u'|ACETOIN|', u'|CARBON-DIOXIDE|']],\n", + " [[u'|MONOMER0-4152|', u'|Protein-Red-Disulfides|'],\n", + " [u'|MONOMER0-4438|', u'|Protein-Ox-Disulfides|']],\n", + " [[u'|AMINO-OXOBUT|', u'|PROTON|'], [u'|AMINO-ACETONE|', u'|CARBON-DIOXIDE|']],\n", + " [[u'|Cytochromes-B-Reduced|', u'|Cytochromes-B|'],\n", + " [u'|Cytochromes-B|', u'|Reduced-Cytochromes-o|']],\n", + " [[u'|L-ASPARTATE|', u'|L-CITRULLINE|', u'|ATP|'],\n", + " [u'|PROTON|', u'|L-ARGININO-SUCCINATE|', u'|PPI|', u'|AMP|']],\n", + " [[u'|CPD-15244|', u'|CO-A|'], [u'|CPD-7221|', u'|ACETYL-COA|']],\n", + " None,\n", + " [[u'|PROTON|', u'|D-BETA-D-HEPTOSE-1-P|', u'|ATP|'],\n", + " [u'|ADP-D-GLYCERO-D-MANNO-HEPTOSE|', u'|PPI|']],\n", + " None]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "direction\n", + "Keyword, Optional Can take on the following values:\n", + "\n", + ":L2R\n", + "The reaction direction goes from ‘left to right’, as described in the \n", + "|Reactions| instance. \n", + ":R2L\n", + "The reaction direction goes from ‘right to left’; the opposite of what is \n", + "described in the |Reactions| instance. \n", + "\n", + "pwy\n", + "Keyword, Optional An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.reaction_reactants_and_products(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + 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(reaction-type '|RXN0-1401| ))\n", + "reaction-type\n", + "(reaction-type '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|SPERMIDINESYN-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7049| ))\n", + "reaction-type\n", + "(reaction-type '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14255| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-1130| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-3221| ))\n", + "reaction-type\n", + "(reaction-type '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|UBIQUINOL-OX-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14882| ))\n", + "reaction-type\n", + "(reaction-type '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|KDO-8PPHOSPHAT-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|DMK-FE-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|DSBDC-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|TAGAALDOL-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7230| ))\n", + "reaction-type\n", + "(reaction-type '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|MEN-FE-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|AMINEPHEN-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7048| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-384| ))\n", + "reaction-type\n", + "(reaction-type '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|ACETATE--COA-LIGASE-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7096| ))\n", + "reaction-type\n", + "(reaction-type '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-15139| ))\n", + "reaction-type\n", + "(reaction-type '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-5068| ))\n", + "reaction-type\n", + "(reaction-type '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|NICONUCADENYLYLTRAN-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2022| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7310| ))\n", + "reaction-type\n", + "(reaction-type '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|THREOSPON-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|CYTC-RED-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|ARGSUCCINSYN-RXN| ))\n", + "reaction-type\n", + "(reaction-type '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14394| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-3141| ))\n", + "reaction-type\n", + "(reaction-type '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-4342| ))\n", + "reaction-type\n", + "(reaction-type '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-type '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|SMALL-MOLECULE|',\n", + " u'|SMALL-MOLECULE|',\n", + " u'|PROTEIN-REACTION|',\n", + " u'|SMALL-MOLECULE|',\n", + " u'|PROTEIN-REACTION|',\n", + " u'|SMALL-MOLECULE|',\n", + " u'|SMALL-MOLECULE|',\n", + " u'|PROTEIN-REACTION|',\n", + " u'|SMALL-MOLECULE|',\n", + " u'|PROTEIN-REACTION|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.reaction_type(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "reaction-without-sequenced-enzyme-p\n", + "(reaction-without-sequenced-enzyme-p '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (reaction-without-sequenced-enzyme-p '|RXN-15348| ))\n" + ] + }, + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_without_sequenced_enzyme_p\u001b[0;34m(self, rxn)\u001b[0m\n\u001b[1;32m 1077\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1078\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1079\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1080\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1081\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 351\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 352\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 353\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 354\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 355\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "complete?\n", + "Optional If true, the predicate will return true when there is any associated \n", + "gene without a sequence. If nil, the predicate will return true when all \n", + "associated genes are without a sequence. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.rxn_without_sequenced_enzyme_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is REACTION-WITHOUT-SEQUENCED-ENZYME-P, \n", + "# which only argument is a rxn" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-15348| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|LACTALDREDUCT-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p 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+ "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DMKCYT-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5061| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|FES-OX-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-16000| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-6505| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PEPCARBOX-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-2601| )\n", + "(with-organism 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"(pathway-hole-p '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-10658| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-16910| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-12473| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-12473| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-2942| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-2942| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-16381| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-16381| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|YIAE2-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|YIAE2-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p 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(pathway-hole-p '|METBALT-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-9533| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-9533| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|PROLINE--TRNA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PROLINE--TRNA-LIGASE-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-9660| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-9660| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|DEOXYADENPHOSPHOR-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DEOXYADENPHOSPHOR-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|SPONTPRO-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|SPONTPRO-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-1144| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-1144| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-5292| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5292| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-5098| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5098| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-17701| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-17701| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|ALCOHOL-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ALCOHOL-DEHYDROG-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-6435| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-6435| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|PYRIDOXINE-4-DEHYDROGENASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PYRIDOXINE-4-DEHYDROGENASE-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-6547| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-6547| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|DIAMACTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) 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))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-14882| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|KDO-8PPHOSPHAT-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DMK-FE-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DSBDC-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|TAGAALDOL-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7230| ))\n", + 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"(pathway-hole-p '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-5068| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|NICONUCADENYLYLTRAN-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-2022| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7310| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|THREOSPON-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|CYTC-RED-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ARGSUCCINSYN-RXN| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-14394| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-3141| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-4342| ))\n", + "pathway-hole-p\n", + "(pathway-hole-p '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "hole-if-any-gene-without-position?\n", + "Keyword, Optional If true, then genes without specified coordinates for the \n", + "current organism’s genome are not counted when determining the status of the \n", + "reaction.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.pathway_hole_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxn-present?\n", + "(rxn-present? '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-present? '|RXN-15348| ))\n" + ] + }, + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1105\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1106\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1107\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1108\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1109\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 351\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 352\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 353\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 354\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 355\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.rxn_present_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is RXN-PRESENT?" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-15348| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-15348| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|LACTALDREDUCT-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|LACTALDREDUCT-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|PFLDEACTIV-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|PFLDEACTIV-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|OHMETPYRKIN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|OHMETPYRKIN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7094| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7094| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|TRIOSEPISOMERIZATION-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|TRIOSEPISOMERIZATION-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7298| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7298| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-1137| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-1137| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|BADH-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|BADH-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|DMKCYT-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|DMKCYT-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-5061| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-5061| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|ACONITATE-DELTA-ISOMERASE-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|ACONITATE-DELTA-ISOMERASE-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|FES-OX-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|FES-OX-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-16000| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-16000| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-6505| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-6505| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|PEPCARBOX-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|PEPCARBOX-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-2601| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-2601| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|MENCYT-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|MENCYT-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|UDP-NACMURALGLDAPAALIG-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|UDP-NACMURALGLDAPAALIG-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7003| '|RXN0-3741| )\n", + "(with-organism 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(rxn-specific-form-of-rxn-p '|RXN0-6389| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-2584| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-2584| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-14503| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-14503| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|IGPSYN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|IGPSYN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|LYXK-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|LYXK-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXNMETA-12671| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXNMETA-12671| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7139| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7139| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|ADENPRIBOSYLTRAN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|ADENPRIBOSYLTRAN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-2941| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-2941| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|5-NUCLEOTID-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|5-NUCLEOTID-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-14569| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-14569| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|MERCAPYSTRANS-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|MERCAPYSTRANS-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-1401| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-1401| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|SPERMIDINESYN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|SPERMIDINESYN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7049| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7049| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|ALCOHOL-DEHYDROG-GENERIC-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|ALCOHOL-DEHYDROG-GENERIC-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-14255| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-14255| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-1130| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-1130| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-3221| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-3221| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|UBIQUINOL-OX-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|UBIQUINOL-OX-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-14882| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-14882| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|KDO-8PPHOSPHAT-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|KDO-8PPHOSPHAT-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|DMK-FE-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|DMK-FE-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|N-ACETYLGLUTPREDUCT-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|N-ACETYLGLUTPREDUCT-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|DSBDC-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|DSBDC-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|TAGAALDOL-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|TAGAALDOL-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7230| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7230| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|MEN-FE-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|MEN-FE-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|AMINEPHEN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|AMINEPHEN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7048| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7048| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-384| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-384| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|ACETATE--COA-LIGASE-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|ACETATE--COA-LIGASE-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7096| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7096| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-15139| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-15139| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-5068| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-5068| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|NICONUCADENYLYLTRAN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|NICONUCADENYLYLTRAN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-2022| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-2022| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-7310| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7310| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|THREOSPON-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|THREOSPON-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|CYTC-RED-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|CYTC-RED-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|ARGSUCCINSYN-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|ARGSUCCINSYN-RXN| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN-14394| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-14394| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-3141| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-3141| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|RXN0-4342| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-4342| '|RXN0-3741| ))\n", + "rxn-specific-form-of-rxn-p\n", + "(rxn-specific-form-of-rxn-p '|DSBD-RXN| '|RXN0-3741| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|DSBD-RXN| '|RXN0-3741| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "specific-rxn\n", + "A child of the class |Reactions|. \n", + "generic-rxn\n", + "A child of the class |Reactions|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.rxn_specific_form_of_rxn_p(specific_rxn = rxn, generic_rxn = u'|RXN0-3741|'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-15348| ))\n", + 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(:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-14569| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|MERCAPYSTRANS-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-1401| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|SPERMIDINESYN-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-7049| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-14255| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-1130| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-3221| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|UBIQUINOL-OX-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-14882| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|KDO-8PPHOSPHAT-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|DMK-FE-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|DSBDC-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|TAGAALDOL-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-7230| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|MEN-FE-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|AMINEPHEN-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-7048| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-384| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|ACETATE--COA-LIGASE-RXN| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-7096| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-15139| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-5068| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|NICONUCADENYLYLTRAN-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-2022| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-7310| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|THREOSPON-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|CYTC-RED-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|ARGSUCCINSYN-RXN| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN-14394| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-3141| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|RXN0-4342| ))\n", + "nonspecific-forms-of-rxn\n", + "(nonspecific-forms-of-rxn '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (nonspecific-forms-of-rxn '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.nonspecific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-15348| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|LACTALDREDUCT-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|PFLDEACTIV-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|OHMETPYRKIN-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7094| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|TRIOSEPISOMERIZATION-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7298| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-1137| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|BADH-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|DMKCYT-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-5061| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|FES-OX-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-16000| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-6505| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|PEPCARBOX-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-2601| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|MENCYT-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7003| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|CARNDETRU-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-14505| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|ADPREDUCT-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-5118| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|CHEBTAPD-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-16650| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|MALATE-DEH-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|DEPHOSICITDEHASE-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|GDPREDUCT-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXNMETA-12672| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|MYRISTOYLACYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|MYRISTOYLACYLTRAN-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|COBINPGUANYLYLTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|COBINPGUANYLYLTRANS-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|PROTEIN-KINASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|PROTEIN-KINASE-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN0-5183| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-5183| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|ADENYL-KIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|ADENYL-KIN-RXN| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-10658| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-10658| ))\n", + "specific-forms-of-rxn\n", + "(specific-forms-of-rxn '|RXN-16910| )\n", + "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-16910| ))\n", + 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"metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.specific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-15348| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-15348| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|LACTALDREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|LACTALDREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PFLDEACTIV-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PFLDEACTIV-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|OHMETPYRKIN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|OHMETPYRKIN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-7094| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7094| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRIOSEPISOMERIZATION-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRIOSEPISOMERIZATION-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-7298| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7298| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-1137| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-1137| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|BADH-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|BADH-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DMKCYT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DMKCYT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5061| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5061| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|ACONITATE-DELTA-ISOMERASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ACONITATE-DELTA-ISOMERASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|FES-OX-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|FES-OX-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-16000| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16000| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-6505| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-6505| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PEPCARBOX-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PEPCARBOX-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-2601| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2601| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|MENCYT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MENCYT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|UDP-NACMURALGLDAPAALIG-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|UDP-NACMURALGLDAPAALIG-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-7003| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7003| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|CARNDETRU-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CARNDETRU-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14505| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14505| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|ADPREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ADPREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5118| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5118| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|CHEBTAPD-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CHEBTAPD-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-16650| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16650| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|MALATE-DEH-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MALATE-DEH-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DEPHOSICITDEHASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DEPHOSICITDEHASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PHENPRODIOLDEHYDROG-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHENPRODIOLDEHYDROG-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|GDPREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|GDPREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|URIDINE-NUCLEOSIDASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|URIDINE-NUCLEOSIDASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXNMETA-12672| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXNMETA-12672| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|MYRISTOYLACYLTRAN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MYRISTOYLACYLTRAN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|COBINPGUANYLYLTRANS-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|COBINPGUANYLYLTRANS-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PROTEIN-KINASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PROTEIN-KINASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5183| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5183| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|ADENYL-KIN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ADENYL-KIN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-10658| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-10658| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-16910| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16910| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-12473| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12473| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-2942| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2942| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-16381| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16381| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|YIAE2-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|YIAE2-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17355| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17355| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|D-PPENTOMUT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|D-PPENTOMUT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14570| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14570| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-19340| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-19340| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5216| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5216| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-5741| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-5741| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17393| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17393| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|METBALT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|METBALT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-9533| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-9533| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PROLINE--TRNA-LIGASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PROLINE--TRNA-LIGASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + 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"(rxn-in-compartment-p '|RXN0-2605| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2605| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17724| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17724| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PHOBR-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHOBR-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-293| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-293| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14510| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14510| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + 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"(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|NARLQ-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-269| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-269| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17489| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17489| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PYFLAVOXRE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PYFLAVOXRE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-295| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-295| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PROPKIN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PROPKIN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-6515| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-6515| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-10660| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-10660| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5230| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5230| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DEOXYINOPHOSPHOR-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DEOXYINOPHOSPHOR-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-13039| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) 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"(rxn-in-compartment-p '|RXN-17753| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17753| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-1147| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-1147| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PYRROLINECARBDEHYDROG-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PYRROLINECARBDEHYDROG-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14992| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14992| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5177| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5177| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p 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'(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|CYSTEINE-AMINOTRANSFERASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CYSTEINE-AMINOTRANSFERASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|1.1.1.264-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|1.1.1.264-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-366| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-366| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5199| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5199| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-58| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-58| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17009| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17009| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-18702| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-18702| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-94| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-94| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PPGPPSYN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PPGPPSYN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-12588| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12588| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DCDPKIN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DCDPKIN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-11589| '(|CCO_CYTOSOL|) )\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-11589| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN0-209| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN0-209| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5228| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5228| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-12894| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12894| '(|CCO_CYTOSOL|) ))\n", + 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'(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14477| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14477| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-126A| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-126A| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-12480| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12480| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRE6PHYDRO-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRE6PHYDRO-RXN| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5202| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) 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))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-11840| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-11840| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-15743| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-15743| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN0-467| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN0-467| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14325| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14325| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|GLUCUROISOM-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|GLUCUROISOM-RXN| 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'|RHAMNULOKIN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RHAMNULOKIN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5268| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5268| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|ASPCARBTRANS-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ASPCARBTRANS-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|THREONINE-ALDOLASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|THREONINE-ALDOLASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-278| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-278| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|ARGSUCCINLYA-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ARGSUCCINLYA-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DSERDEAM-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DSERDEAM-RXN| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-297| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-297| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5039| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5039| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-4341| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-4341| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + 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(rxn-in-compartment-p '|TRANS-RXN-155| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-19854| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-19854| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14904| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14904| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5205| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5205| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|NACGLCTRANS-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|NACGLCTRANS-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|KETOGLUTREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", + 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"rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|3.1.13.1-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|3.1.13.1-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-5330| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5330| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-6081| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-6081| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-16420| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16420| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-296| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-296| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-2382| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2382| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-12753| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12753| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-33| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-33| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|GMP-REDUCT-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|GMP-REDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|PGLYCEROLTRANSII-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PGLYCEROLTRANSII-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + 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)\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|UDPSUGARHYDRO-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-367| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-367| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|LYSOPHOSPHOLIPASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|LYSOPHOSPHOLIPASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-7948| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-7948| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN-61| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN-61| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-13142| '(|CCO_CYTOSOL|) )\n", + "(with-organism 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(rxn-in-compartment-p '|LYSINE--TRNA-LIGASE-RXN| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-17636| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17636| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|FRUCTOKINASE-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|FRUCTOKINASE-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|TRANS-RXN0-501| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRANS-RXN0-501| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-986| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-986| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-6482| '(|CCO_CYTOSOL|) )\n", + 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'|ARGSUCCINSYN-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ARGSUCCINSYN-RXN| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN-14394| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14394| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-3141| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-3141| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|RXN0-4342| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-4342| '(|CCO_CYTOSOL|) ))\n", + "rxn-in-compartment-p\n", + "(rxn-in-compartment-p '|DSBD-RXN| '(|CCO_CYTOSOL|) )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DSBD-RXN| '(|CCO_CYTOSOL|) ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.rxn_in_compartment_p(rxn = rxn, compartments = [u'|CCO_CYTOSOL|']))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "compartment-of-rxn\n", + "(compartment-of-rxn '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (compartment-of-rxn '|RXN-15348| ))\n" + ] + }, + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1204\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCCO\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1205\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1206\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1207\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1208\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "default\n", + "Optional The default compartment for reactions without any compartment \n", + "annotations on their substrates. The default value is 'CCO‑CYTOSOL. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.compartment_of_rxn(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is missing (?)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-15348| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|LACTALDREDUCT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PFLDEACTIV-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|OHMETPYRKIN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7094| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7298| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1137| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|BADH-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DMKCYT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-5061| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5061| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|FES-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|FES-OX-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-16000| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16000| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-6505| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-6505| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|PEPCARBOX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PEPCARBOX-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-2601| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2601| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|MENCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MENCYT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7003| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7003| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|CARNDETRU-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CARNDETRU-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14505| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14505| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ADPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ADPREDUCT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-5118| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5118| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|CHEBTAPD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CHEBTAPD-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-16650| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16650| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|MALATE-DEH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MALATE-DEH-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DEPHOSICITDEHASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DEPHOSICITDEHASE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|PHENPRODIOLDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PHENPRODIOLDEHYDROG-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|GDPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|GDPREDUCT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXNMETA-12672| )\n", + "(with-organism (:org-id '|ECOLI|) 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"(compartments-of-reaction '|RXN-17775| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17775| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|5-FORMYL-THF-CYCLO-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|5-FORMYL-THF-CYCLO-LIGASE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-13854| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-13854| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|PYRUVATEDECARB-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PYRUVATEDECARB-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-1382| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1382| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DIHYDROFOLATESYNTH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DIHYDROFOLATESYNTH-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14251| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14251| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|HISTAMINOTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|HISTAMINOTRANS-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-5408| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5408| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|KDGALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|KDGALDOL-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-17791| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17791| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7229| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7229| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7078| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7078| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RHAMNULPALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RHAMNULPALDOL-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ACETALD-DEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACETALD-DEHYDROG-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DTDPDEHYDRHAMEPIM-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DTDPDEHYDRHAMEPIM-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-2001| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2001| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|3.4.24.55-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|3.4.24.55-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-5515| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5515| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14393| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14393| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-17905| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17905| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|LACTALDDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|LACTALDDEHYDROG-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-9311| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-9311| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-10016| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-10016| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7291| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7291| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ERYTH4PDEHYDROG-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ERYTH4PDEHYDROG-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ACNEULY-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACNEULY-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14113| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14113| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-6389| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-6389| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-2584| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2584| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14503| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14503| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|IGPSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|IGPSYN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|LYXK-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|LYXK-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXNMETA-12671| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXNMETA-12671| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7139| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7139| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ADENPRIBOSYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ADENPRIBOSYLTRAN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-2941| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2941| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|5-NUCLEOTID-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|5-NUCLEOTID-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14569| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14569| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|MERCAPYSTRANS-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MERCAPYSTRANS-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-1401| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1401| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|SPERMIDINESYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|SPERMIDINESYN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7049| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7049| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14255| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14255| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-1130| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1130| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-3221| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-3221| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|UBIQUINOL-OX-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|UBIQUINOL-OX-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14882| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14882| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|KDO-8PPHOSPHAT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|KDO-8PPHOSPHAT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DMK-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DMK-FE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DSBDC-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DSBDC-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|TAGAALDOL-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|TAGAALDOL-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7230| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7230| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|MEN-FE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MEN-FE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|AMINEPHEN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|AMINEPHEN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7048| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7048| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-384| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-384| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7096| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7096| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-15139| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-5068| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2022| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7310| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|THREOSPON-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CYTC-RED-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ARGSUCCINSYN-RXN| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14394| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-3141| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-4342| ))\n", + "compartments-of-reaction\n", + "(compartments-of-reaction '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-PERI-BAC|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-CYTOSOL|'],\n", + " [u'|CCO-PERI-BAC|']]" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "sides\n", + "Keyword, Optional The slots of the reaction to consider. The default value is \n", + "'(LEFT RIGHT). \n", + "default-compartment\n", + "The default compartment, as determined by the function (default‑compartment), \n", + "which currently is set to 'CCO‑CYTOSOL.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.compartments_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::transport )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::transport ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-145| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-145| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-7221| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-7221| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-212| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-212| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-108G| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-108G| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-168| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-168| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-1982| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-1982| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-126A| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-126A| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-242| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-242| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|ABC-23-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|ABC-23-RXN| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-265| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-265| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-5202| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-5202| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-283| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-283| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-505| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-505| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-7050| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-7050| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-181A| )\n", + "(with-organism 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'|TRANS-RXN0-244| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-244| ))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-122A| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-122A| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-239| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-239| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-238| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-238| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-502| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-502| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-7041| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-7041| ))\n", + 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(transported-chemicals '|TRANS-RXN0-617| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-7199| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-7199| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-62A| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-62A| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-578| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-578| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-108E| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-108E| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|RXN0-1701| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-1701| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-600| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-600| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-123| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-123| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN0-491| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN0-491| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-94B| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-94B| ))\n", + "transported-chemicals\n", + "(transported-chemicals '|TRANS-RXN-1| )\n", + "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-1| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|Nucleosides|'],\n", + " [u'|D-ALANINE|', u'|PROTON|'],\n", + " [u'|GUANINE|'],\n", + " [u'|DEOXYINOSINE|', u'|PROTON|'],\n", + " [u'|PROTON|', u'|CPD0-2241|'],\n", + " [u'|Inorganic-Compounds|'],\n", + " [u'|PROTON|', u'|D-GALACTURONATE|'],\n", + " [u'|CPD0-2486|'],\n", + " [u'|MELIBIOSE|', u'|LI+|'],\n", + " [u'|FORMATE|']]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "side\n", + "Keyword, Optional The side of the reaction from which to return the transported \n", + "compound. \n", + "primary-only?\n", + "Keyword, Optional If true, then filter out common exchangers (currently defined \n", + "as '(PROTON NA CPD-1)+). If true, and the only transported compounds are in this \n", + "list, then the filter doesn’t apply. \n", + "from-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported from that compartment. \n", + "to-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported to that compartment. \n", + "show-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, and the \n", + "compound is modified during transport, then only return the form of the compound \n", + "as found in this compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':transport'):\n", + " lst.append(ecoli.transported_chemicals(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-15348| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-15348| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|LACTALDREDUCT-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|LACTALDREDUCT-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|PFLDEACTIV-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|PFLDEACTIV-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|OHMETPYRKIN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|OHMETPYRKIN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7094| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7094| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|TRIOSEPISOMERIZATION-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|TRIOSEPISOMERIZATION-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7298| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7298| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-1137| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-1137| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|BADH-RXN| 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))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-13854| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-13854| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|PYRUVATEDECARB-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|PYRUVATEDECARB-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-1382| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-1382| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|DIHYDROFOLATESYNTH-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|DIHYDROFOLATESYNTH-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-14251| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14251| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|HISTAMINOTRANS-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors 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'|ECOLI|) (get-predecessors '|ERYTH4PDEHYDROG-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|ACNEULY-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|ACNEULY-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-14113| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14113| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-6389| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-6389| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-2584| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-2584| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-14503| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14503| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|IGPSYN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|IGPSYN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|LYXK-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|LYXK-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXNMETA-12671| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXNMETA-12671| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7139| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7139| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|ADENPRIBOSYLTRAN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|ADENPRIBOSYLTRAN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-2941| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-2941| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|5-NUCLEOTID-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|5-NUCLEOTID-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-14569| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14569| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|MERCAPYSTRANS-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|MERCAPYSTRANS-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-1401| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-1401| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|SPERMIDINESYN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|SPERMIDINESYN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7049| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7049| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|ALCOHOL-DEHYDROG-GENERIC-RXN| 'PWY0-1347 )\n", + 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)\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|KDO-8PPHOSPHAT-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|DMK-FE-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|DMK-FE-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|N-ACETYLGLUTPREDUCT-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|N-ACETYLGLUTPREDUCT-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|DSBDC-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|DSBDC-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|TAGAALDOL-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|TAGAALDOL-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7230| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7230| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|MEN-FE-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|MEN-FE-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|AMINEPHEN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|AMINEPHEN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7048| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7048| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-384| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-384| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|ACETATE--COA-LIGASE-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|ACETATE--COA-LIGASE-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7096| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7096| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-15139| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-15139| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-5068| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-5068| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|NICONUCADENYLYLTRAN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|NICONUCADENYLYLTRAN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-2022| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-2022| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-7310| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-7310| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|THREOSPON-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|THREOSPON-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|CYTC-RED-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|CYTC-RED-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|ARGSUCCINSYN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|ARGSUCCINSYN-RXN| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN-14394| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14394| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-3141| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-3141| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|RXN0-4342| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-4342| 'PWY0-1347 ))\n", + "get-predecessors\n", + "(get-predecessors '|DSBD-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-predecessors '|DSBD-RXN| 'PWY0-1347 ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.get_predecessors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "get-successors\n", + "(get-successors '|RXN-15348| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-15348| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|LACTALDREDUCT-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|LACTALDREDUCT-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|PFLDEACTIV-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|PFLDEACTIV-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|OHMETPYRKIN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|OHMETPYRKIN-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-7094| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-7094| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|TRIOSEPISOMERIZATION-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|TRIOSEPISOMERIZATION-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-7298| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-7298| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-1137| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors 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))\n", + "get-successors\n", + "(get-successors '|RXN-16910| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-16910| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN-12473| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-12473| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-2942| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-2942| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN-16381| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-16381| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|YIAE2-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|YIAE2-RXN| 'PWY0-1347 ))\n", + 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"(get-successors '|RXN0-6435| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-6435| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|PYRIDOXINE-4-DEHYDROGENASE-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|PYRIDOXINE-4-DEHYDROGENASE-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-6547| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-6547| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|DIAMACTRANS-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|DIAMACTRANS-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-3241| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-3241| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-745| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-745| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors 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"(get-successors '|ARGSUCCINSYN-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|ARGSUCCINSYN-RXN| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN-14394| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-14394| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-3141| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-3141| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|RXN0-4342| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-4342| 'PWY0-1347 ))\n", + "get-successors\n", + "(get-successors '|DSBD-RXN| 'PWY0-1347 )\n", + "(with-organism (:org-id '|ECOLI|) (get-successors '|DSBD-RXN| 'PWY0-1347 ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.get_successors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN-15348| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN-15348| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|LACTALDREDUCT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|LACTALDREDUCT-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|PFLDEACTIV-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|PFLDEACTIV-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|OHMETPYRKIN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|OHMETPYRKIN-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-7094| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-7094| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|TRIOSEPISOMERIZATION-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|TRIOSEPISOMERIZATION-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-7298| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-7298| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-1137| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-1137| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|BADH-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|BADH-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|DMKCYT-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|DMKCYT-RXN| ))\n", + 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))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN-15139| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN-15139| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN-5068| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN-5068| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|NICONUCADENYLYLTRAN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|NICONUCADENYLYLTRAN-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-2022| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-2022| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-7310| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-7310| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|THREOSPON-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|THREOSPON-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|CYTC-RED-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|CYTC-RED-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|ARGSUCCINSYN-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|ARGSUCCINSYN-RXN| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN-14394| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN-14394| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-3141| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-3141| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|RXN0-4342| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-4342| ))\n", + "rxn-w-isozymes-p\n", + "(rxn-w-isozymes-p '|DSBD-RXN| )\n", + "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|DSBD-RXN| ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, True, False, False, False]" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type = ':all'):\n", + " lst.append(ecoli.rxn_w_isozymes_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Regulation Frames.ipynb b/examples/ptools API - Operations on Regulation Frames.ipynb new file mode 100644 index 0000000..9a089b8 --- /dev/null +++ b/examples/ptools API - Operations on Regulation Frames.ipynb @@ -0,0 +1,1411 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", + "[u'|META|', u'|ECOLI|']\n", + "class-name-p\n", + "(class-name-p \"regulation\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"regulation\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Regulation| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Regulation| ))\n", + "get-class\n", + "(get-class |Regulation| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Regulation| ))\n", + "class-name-p\n", + "(class-name-p \"genes\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"genes\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Genes| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Genes| ))\n", + "get-class\n", + "(get-class |Genes| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Genes| ))\n", + "class-name-p\n", + "(class-name-p \"proteins\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"proteins\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Proteins| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Proteins| ))\n", + "get-class\n", + "(get-class |Proteins| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Proteins| ))\n", + "class-name-p\n", + "(class-name-p \"transcription_units\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"transcription_units\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Transcription-Units| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Transcription-Units| ))\n", + "get-class\n", + "(get-class |Transcription-Units| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Transcription-Units| ))\n", + "class-name-p\n", + "(class-name-p \"DNA_Binding_Sites\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"DNA_Binding_Sites\" ))\n", + "get-frame-object\n", + "(get-frame-object '|DNA-Binding-Sites| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|DNA-Binding-Sites| ))\n", + "get-class\n", + "(get-class |DNA-Binding-Sites| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |DNA-Binding-Sites| ))\n", + "class-name-p\n", + "(class-name-p \"mRNA_Binding_Sites\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"mRNA_Binding_Sites\" ))\n", + "get-frame-object\n", + "(get-frame-object '|mRNA-Binding-Sites| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|mRNA-Binding-Sites| ))\n", + "get-class\n", + "(get-class |mRNA-Binding-Sites| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |mRNA-Binding-Sites| ))\n", + "class-name-p\n", + "(class-name-p \"Terminators\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"Terminators\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Terminators| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Terminators| ))\n", + "get-class\n", + "(get-class |Terminators| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Terminators| ))\n", + "class-name-p\n", + "(class-name-p \"Promoters\" )\n", + "(with-organism (:org-id '|ECOLI|) (class-name-p \"Promoters\" ))\n", + "get-frame-object\n", + "(get-frame-object '|Promoters| )\n", + "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Promoters| ))\n", + "get-class\n", + "(get-class |Promoters| )\n", + "(with-organism (:org-id '|ECOLI|) (get-class |Promoters| ))\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "\n", + "regs = [x.frameid for x in ecoli.regulation.instances][0:2]\n", + "genes = [x.frameid for x in ecoli.genes.instances][0:2]\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "tus = [x.frameid for x in ecoli.transcription_units.instances][0:2]\n", + "dna_sites = [x.frameid for x in ecoli.DNA_Binding_Sites.instances][0:2]\n", + "mrna_sites = [x.frameid for x in ecoli.mRNA_Binding_Sites.instances][0:2]\n", + "terminators = [x.frameid for x in ecoli.Terminators.instances][0:2]\n", + "promoters = [x.frameid for x in ecoli.Promoters.instances][0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "activation-p\n", + "(activation-p '|REG0-5116| )\n", + "(with-organism (:org-id '|ECOLI|) (activation-p '|REG0-5116| ))\n", + "activation-p\n", + "(activation-p '|REG0-5024| )\n", + "(with-organism (:org-id '|ECOLI|) (activation-p '|REG0-5024| ))\n", + "[True, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.activation_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "inhibition-p\n", + "(inhibition-p '|REG0-5116| )\n", + "(with-organism (:org-id '|ECOLI|) (inhibition-p '|REG0-5116| ))\n", + "inhibition-p\n", + "(inhibition-p '|REG0-5024| )\n", + "(with-organism (:org-id '|ECOLI|) (inhibition-p '|REG0-5024| ))\n", + "[False, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.inhibition_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "direct-regulators\n", + "(direct-regulators '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-regulators '|EG11414| ))\n", + "direct-regulators\n", + "(direct-regulators '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-regulators '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "direct-activators\n", + "(direct-activators '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-activators '|EG11414| ))\n", + "direct-activators\n", + "(direct-activators '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-activators '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_activators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "direct-inhibitors\n", + "(direct-inhibitors '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-inhibitors '|EG11414| ))\n", + "direct-inhibitors\n", + "(direct-inhibitors '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (direct-inhibitors '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_inhibitors(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-factor?\n", + "(transcription-factor? '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-factor? '|OPPC-MONOMER| ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_p(protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulator-of-type?\n", + "(regulator-of-type? '|OPPC-MONOMER| :activator )\n", + "(with-organism (:org-id '|ECOLI|) (regulator-of-type? '|OPPC-MONOMER| :activator ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.regulator_of_type(protein, class_name = ':activator'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulon-of-protein\n", + "(regulon-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (regulon-of-protein '|OPPC-MONOMER| ))\n", + "regulon-of-protein\n", + "(regulon-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (regulon-of-protein '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.regulon_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulation-frame-transcription-units\n", + "(regulation-frame-transcription-units '|REG0-5116| )\n", + "(with-organism (:org-id '|ECOLI|) (regulation-frame-transcription-units '|REG0-5116| ))\n", + "regulation-frame-transcription-units\n", + "(regulation-frame-transcription-units '|REG0-5024| )\n", + "(with-organism (:org-id '|ECOLI|) (regulation-frame-transcription-units '|REG0-5024| ))\n", + "[[u'|TU162|'], [u'|TU461|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.regulation_frame_transcription_units(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-regulation-frames\n", + "(transcription-unit-regulation-frames '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-regulation-frames '|TU0-8814| ))\n", + "transcription-unit-regulation-frames\n", + "(transcription-unit-regulation-frames '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-regulation-frames '|TU0-8340| ))\n", + "[[], [u'|REG0-11053|', u'|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_regulation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-activation-frames\n", + "(transcription-unit-activation-frames '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-activation-frames '|TU0-8814| ))\n", + "transcription-unit-activation-frames\n", + "(transcription-unit-activation-frames '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-activation-frames '|TU0-8340| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-inhibition-frames\n", + "(transcription-unit-inhibition-frames '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibition-frames '|TU0-8814| ))\n", + "transcription-unit-inhibition-frames\n", + "(transcription-unit-inhibition-frames '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibition-frames '|TU0-8340| ))\n", + "[[], [u'|REG0-11053|', u'|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibition_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-units-of-protein\n", + "(transcription-units-of-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-units-of-protein '|OPPC-MONOMER| ))\n", + "transcription-units-of-protein\n", + "(transcription-units-of-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-units-of-protein '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_units_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-regulated-by-protein\n", + "(genes-regulated-by-protein '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-protein '|OPPC-MONOMER| ))\n", + "genes-regulated-by-protein\n", + "(genes-regulated-by-protein '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-protein '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_regulated_by_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "DNA-binding-sites-of-protein\n", + "(DNA-binding-sites-of-protein '|OPPC-MONOMER| :all-forms? t)\n", + "(with-organism (:org-id '|ECOLI|) (DNA-binding-sites-of-protein '|OPPC-MONOMER| :all-forms? t))\n", + "DNA-binding-sites-of-protein\n", + "(DNA-binding-sites-of-protein '|YHBN-MONOMER| :all-forms? t)\n", + "(with-organism (:org-id '|ECOLI|) (DNA-binding-sites-of-protein '|YHBN-MONOMER| :all-forms? t))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.DNA_binding_sites_of_protein(protein, all_forms = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulator-proteins-of-transcription-unit\n", + "(regulator-proteins-of-transcription-unit '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (regulator-proteins-of-transcription-unit '|TU0-8814| ))\n", + "regulator-proteins-of-transcription-unit\n", + "(regulator-proteins-of-transcription-unit '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (regulator-proteins-of-transcription-unit '|TU0-8340| ))\n", + "[[], [u'|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulator_proteins_of_transcription_unit(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-factor-ligands\n", + "(transcription-factor-ligands '|OPPC-MONOMER| ::both )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-factor-ligands '|OPPC-MONOMER| ::both ))\n" + ] + } + ], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_ligands(protein, u':both'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-factor-active-forms\n", + "(transcription-factor-active-forms '|OPPC-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-factor-active-forms '|OPPC-MONOMER| ))\n", + "transcription-factor-active-forms\n", + "(transcription-factor-active-forms '|YHBN-MONOMER| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-factor-active-forms '|YHBN-MONOMER| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_active_forms(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-regulating-gene\n", + "(genes-regulating-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulating-gene '|EG11414| ))\n", + "genes-regulating-gene\n", + "(genes-regulating-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulating-gene '|EG11127| ))\n", + "[[], [u'|G6761|', u'|EG10457|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulating_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "genes-regulated-by-gene\n", + "(genes-regulated-by-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-gene '|EG11414| ))\n", + "genes-regulated-by-gene\n", + "(genes-regulated-by-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-gene '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulated_by_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulators-of-gene\n", + "(regulators-of-gene '|EG11414| :by-function? t)\n", + "(with-organism (:org-id '|ECOLI|) (regulators-of-gene '|EG11414| :by-function? t))\n", + "regulators-of-gene\n", + "(regulators-of-gene '|EG11127| :by-function? t)\n", + "(with-organism (:org-id '|ECOLI|) (regulators-of-gene '|EG11127| :by-function? t))\n", + "[[None, None, None], [[u'|G6761-MONOMER|'], [u'|PD00288|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.regulators_of_gene_transcription(gene, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-activators\n", + "(transcription-unit-activators '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-activators '|TU0-8814| ))\n", + "transcription-unit-activators\n", + "(transcription-unit-activators '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-activators '|TU0-8340| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-inhibitors\n", + "(transcription-unit-inhibitors '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibitors '|TU0-8814| ))\n", + "transcription-unit-inhibitors\n", + "(transcription-unit-inhibitors '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibitors '|TU0-8340| ))\n", + "[[], [u'|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibitors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "regulators-of-operon-transcription\n", + "(regulators-of-operon-transcription '(|TU0-8814|) t )\n", + "(with-organism (:org-id '|ECOLI|) (regulators-of-operon-transcription '(|TU0-8814|) t ))\n", + "regulators-of-operon-transcription\n", + "(regulators-of-operon-transcription '(|TU0-8340|) t )\n", + "(with-organism (:org-id '|ECOLI|) (regulators-of-operon-transcription '(|TU0-8340|) t ))\n", + "[[None, None, None], [None, [u'|PD01379|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulators_of_operon_transcription(tu, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-promoter\n", + "(transcription-unit-promoter '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-promoter '|TU0-8814| ))\n", + "transcription-unit-promoter\n", + "(transcription-unit-promoter '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-promoter '|TU0-8340| ))\n", + "[None, u'|PM0-8720|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_promoter(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-genes\n", + "(transcription-unit-genes '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-genes '|TU0-8814| ))\n", + "transcription-unit-genes\n", + "(transcription-unit-genes '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-genes '|TU0-8340| ))\n", + "[[u'|G6954|'], [u'|EG11346|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_genes(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-first-gene\n", + "(transcription-unit-first-gene '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-first-gene '|TU0-8814| ))\n", + "transcription-unit-first-gene\n", + "(transcription-unit-first-gene '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-first-gene '|TU0-8340| ))\n", + "[u'|G6954|', u'|EG11346|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_first_gene(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-binding-sites\n", + "(transcription-unit-binding-sites '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-binding-sites '|TU0-8814| ))\n", + "transcription-unit-binding-sites\n", + "(transcription-unit-binding-sites '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-binding-sites '|TU0-8340| ))\n", + "[[], [u'|BS0-8048|', u'|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-transcription-factors\n", + "(transcription-unit-transcription-factors '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-transcription-factors '|TU0-8814| ))\n", + "transcription-unit-transcription-factors\n", + "(transcription-unit-transcription-factors '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-transcription-factors '|TU0-8340| ))\n", + "[[], [u'|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_transcription_factors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-mrna-binding-sites\n", + "(transcription-unit-mrna-binding-sites '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-mrna-binding-sites '|TU0-8814| ))\n", + "transcription-unit-mrna-binding-sites\n", + "(transcription-unit-mrna-binding-sites '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-mrna-binding-sites '|TU0-8340| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_mrna_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chromosome-of-operon\n", + "(chromosome-of-operon '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-operon '|TU0-8814| ))\n", + "chromosome-of-operon\n", + "(chromosome-of-operon '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (chromosome-of-operon '|TU0-8340| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.chromosome_of_operon(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "binding-sites-affecting-gene\n", + "(binding-sites-affecting-gene '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-sites-affecting-gene '|EG11414| ))\n", + "binding-sites-affecting-gene\n", + "(binding-sites-affecting-gene '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-sites-affecting-gene '|EG11127| ))\n", + "[[], [u'|BS0-7937|', u'|BS0-7936|', u'|BS0-7935|', u'|BS0-7225|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_sites_affecting_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "binding-site->regulators\n", + "(binding-site->regulators '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|EG11414| ))\n", + "binding-site->regulators\n", + "(binding-site->regulators '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|EG11127| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_site_to_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "binding-site->regulators\n", + "(binding-site->regulators '|BS0-1683| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|BS0-1683| ))\n", + "binding-site->regulators\n", + "(binding-site->regulators '|BS0-8256| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|BS0-8256| ))\n", + "[[u'|PHOSPHO-PHOB|'], [u'|CPLX0-7639|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_to_regulators(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-units-of-promoter\n", + "(transcription-units-of-promoter '|PM0-10506| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-units-of-promoter '|PM0-10506| ))\n", + "transcription-units-of-promoter\n", + "(transcription-units-of-promoter '|PM0-10035| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-units-of-promoter '|PM0-10035| ))\n", + "[[u'|TU0-13975|'], [u'|TU0-8636|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.transcription_units_of_promoter(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "promoter-binding-sites\n", + "(promoter-binding-sites '|PM0-10506| )\n", + "(with-organism (:org-id '|ECOLI|) (promoter-binding-sites '|PM0-10506| ))\n", + "promoter-binding-sites\n", + "(promoter-binding-sites '|PM0-10035| )\n", + "(with-organism (:org-id '|ECOLI|) (promoter-binding-sites '|PM0-10035| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.promoter_binding_sites(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-terminators\n", + "(transcription-unit-terminators '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-terminators '|TU0-8814| ))\n", + "transcription-unit-terminators\n", + "(transcription-unit-terminators '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-terminators '|TU0-8340| ))\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_terminators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "containing-tus\n", + "(containing-tus '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|TU0-8814| ))\n", + "containing-tus\n", + "(containing-tus '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|TU0-8340| ))\n", + "[[u'|TU0-8814|'], [u'|TU0-8340|']]\n", + "containing-tus\n", + "(containing-tus '|RBS0-212| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|RBS0-212| ))\n", + "containing-tus\n", + "(containing-tus '|RBS0-96| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|RBS0-96| ))\n", + "[[u'|TU0-42642|', u'|TU0-42640|', u'|TU0-42638|', u'|TU0-42636|', u'|TU281|', u'|TU00342|'], [u'|TU00392|']]\n", + "containing-tus\n", + "(containing-tus '|BS0-1683| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|BS0-1683| ))\n", + "containing-tus\n", + "(containing-tus '|BS0-8256| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|BS0-8256| ))\n", + "[[u'|TU0-2021|'], [u'|TU0-13514|']]\n", + "containing-tus\n", + "(containing-tus '|PM0-10506| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|PM0-10506| ))\n", + "containing-tus\n", + "(containing-tus '|PM0-10035| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|PM0-10035| ))\n", + "[[u'|TU0-13975|'], [u'|TU0-8636|']]\n", + "containing-tus\n", + "(containing-tus '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|EG11414| ))\n", + "containing-tus\n", + "(containing-tus '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|EG11127| ))\n", + "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-13193|']]\n", + "containing-tus\n", + "(containing-tus '|TERM1| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|TERM1| ))\n", + "containing-tus\n", + "(containing-tus '|TERM0881| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-tus '|TERM0881| ))\n", + "[[u'|TU-8390|', u'|TU-8389|'], [u'|TU00091|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "containing-chromosome\n", + "(containing-chromosome '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TU0-8814| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TU0-8340| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n", + "containing-chromosome\n", + "(containing-chromosome '|RBS0-212| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|RBS0-212| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|RBS0-96| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|RBS0-96| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n", + "containing-chromosome\n", + "(containing-chromosome '|BS0-1683| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|BS0-1683| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|BS0-8256| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|BS0-8256| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n", + "containing-chromosome\n", + "(containing-chromosome '|PM0-10506| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|PM0-10506| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|PM0-10035| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|PM0-10035| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n", + "containing-chromosome\n", + "(containing-chromosome '|EG11414| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|EG11414| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|EG11127| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|EG11127| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n", + "containing-chromosome\n", + "(containing-chromosome '|TERM1| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TERM1| ))\n", + "containing-chromosome\n", + "(containing-chromosome '|TERM0881| )\n", + "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TERM0881| ))\n", + "[u'|COLI-K12|', u'|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "binding-site-promoters\n", + "(binding-site-promoters '|BS0-1683| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-promoters '|BS0-1683| ))\n", + "binding-site-promoters\n", + "(binding-site-promoters '|BS0-8256| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-promoters '|BS0-8256| ))\n", + "[[u'|PM0-2201|'], [u'|PM0-9620|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_promoters(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "transcription-unit-all-components\n", + "(transcription-unit-all-components '|TU0-8814| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-all-components '|TU0-8814| ))\n", + "transcription-unit-all-components\n", + "(transcription-unit-all-components '|TU0-8340| )\n", + "(with-organism (:org-id '|ECOLI|) (transcription-unit-all-components '|TU0-8340| ))\n", + "[[u'|G6954|'], [u'|PM0-8720|', u'|EG11346|', u'|BS0-8048|', u'|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_all_components(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "binding-site-transcription-units\n", + "(binding-site-transcription-units '|BS0-1683| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|BS0-1683| ))\n", + "binding-site-transcription-units\n", + "(binding-site-transcription-units '|BS0-8256| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|BS0-8256| ))\n", + "[[u'|TU0-2021|'], [u'|TU0-13514|']]\n", + "binding-site-transcription-units\n", + "(binding-site-transcription-units '|RBS0-212| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|RBS0-212| ))\n", + "binding-site-transcription-units\n", + "(binding-site-transcription-units '|RBS0-96| )\n", + "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|RBS0-96| ))\n", + "[[u'|TU0-42642|', u'|TU0-42640|', u'|TU0-42638|', u'|TU0-42636|', u'|TU281|', u'|TU00342|'], [u'|TU00392|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(dna_site))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for mrna_site in mrna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(mrna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - enumeration operations.ipynb b/examples/ptools API - enumeration operations.ipynb new file mode 100644 index 0000000..baf7523 --- /dev/null +++ b/examples/ptools API - enumeration operations.ipynb @@ -0,0 +1,926 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", + "sys.path = [module_path]\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[u'|META|', u'|ECOLI|']\n" + ] + } + ], + "source": [ + "# remove pyc files\n", + "!rm ./PythonCyc/pythoncyc/*pyc\n", + "\n", + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print all_orgids\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-pathways\n", + "(all-pathways ::all t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", + "all-pathways\n", + "(all-pathways ::small-molecule t )\n", + "(with-organism (:org-id '|ECOLI|) (all-pathways ::small-molecule t ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|PWY0-1347|',\n", + " u'|PWY-6690|',\n", + " u'|PWY0-1348|',\n", + " u'|PWY-5162|',\n", + " u'|PWY0-1352|',\n", + " u'|PWY0-1355|',\n", + " u'|2PHENDEG-PWY|',\n", + " u'|PWY0-1465|',\n", + " u'|TRESYN-PWY|',\n", + " u'|PANTO-PWY|']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "selector\n", + "Optional Selects whether all pathways, or just small-molecule metabolism base \n", + "pathways. Can take either a symbol of :all or :small‑molecule. Defaults to \n", + ":all. \n", + "base?\n", + "Optional If this argument evaluates to true, only includes base pathways. \n", + "Otherwise, all pathways, including superpathways, will be returned. \n", + "\"\"\"\n", + "\n", + "ecoli.all_pathways(selector = u':all', base = True)[0:10]\n", + "ecoli.all_pathways(selector = u':small-molecule', base = True)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", + "all-rxns\n", + "(all-rxns ::metab-pathways )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-pathways ))\n", + "all-rxns\n", + "(all-rxns ::metab-smm )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-smm ))\n", + "all-rxns\n", + "(all-rxns ::metab-all )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-all ))\n", + "all-rxns\n", + "(all-rxns ::transport )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::transport ))\n", + "all-rxns\n", + "(all-rxns ::small-molecule )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::small-molecule ))\n", + "all-rxns\n", + "(all-rxns ::protein-small-molecule-reaction )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::protein-small-molecule-reaction ))\n", + "all-rxns\n", + "(all-rxns ::protein-reaction )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::protein-reaction ))\n", + "all-rxns\n", + "(all-rxns ::trna-reaction )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::trna-reaction ))\n", + "all-rxns\n", + "(all-rxns ::spontaneous )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::spontaneous ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|RXN-17635|',\n", + " u'|RXN-6268|',\n", + " u'|RXN-7282|',\n", + " u'|RXN-10720|',\n", + " u'|RXN-12870|',\n", + " u'|RXN-14515|',\n", + " u'|RXN-13460|',\n", + " u'|RXN-14808|',\n", + " u'|RXN-18819|',\n", + " u'|RXN-15121|']" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Optional The type of reaction to return. Defaults to :metab‑smm. The possible \n", + "values are:\n", + "\n", + ":all\n", + "All reactions. \n", + ":metab-pathways\n", + "All reactions found within metabolic pathways. Includes reactions that are \n", + "pathway holes. May include a handfull of reactions whose substrates are \n", + "macromolecules, e.g., ACP. Excludes transport reactions. \n", + ":metab-smm\n", + "All reactions of small molecule metabolism, whether or not they are present in a \n", + "pathway. Subsumes :metab‑pathways. \n", + ":metab-all\n", + "All enzyme-catalyzed reactions. Subsumes :metab‑smm. \n", + ":enzyme\n", + "All enzyme-catalyzed reactions (i.e., instances of either EC-Reactions class or \n", + "Unclassified-Reactions class). \n", + ":transport\n", + "All transport reactions. \n", + ":small-molecule\n", + "All reactions whose substrates are all small molecules, as opposed to \n", + "macromolecules. Excludes transport reactions. \n", + ":protein-small-molecule-reaction\n", + "One of the substrates of the reaction is a macromolecule, and one of the \n", + "substrates of the reaction is a small molecule. \n", + ":protein-reaction\n", + "All substrates of the reaction are proteins. \n", + ":trna-reaction\n", + "One of the substrates of the reaction is a tRNA. \n", + ":spontaneous\n", + "Spontaneous reactions. \n", + ":non-spontaneous\n", + "Non-spontaneous reactions that are likely to be enzyme catalyzed. Some reactions \n", + "will be returned for type :non‑spontaneous that will not be returned by \n", + ":enzyme. \n", + "\"\"\"\n", + "\n", + "ecoli.all_rxns(type = ':all')[0:10]\n", + "ecoli.all_rxns(type = ':metab-pathways')[0:10]\n", + "ecoli.all_rxns(type = ':metab-smm')[0:10]\n", + "ecoli.all_rxns(type = ':metab-all')[0:10]\n", + "ecoli.all_rxns(type = ':transport')[0:10]\n", + "ecoli.all_rxns(type = ':small-molecule')[0:10]\n", + "ecoli.all_rxns(type = ':protein-small-molecule-reaction')[0:10]\n", + "ecoli.all_rxns(type = ':protein-reaction')[0:10]\n", + "ecoli.all_rxns(type = ':trna-reaction')[0:10]\n", + "ecoli.all_rxns(type = ':spontaneous')[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::spontaneous )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::spontaneous ))\n", + "all-substrates\n", + "(all-substrates '(|RXN-17635|) )\n", + "(with-organism (:org-id '|ECOLI|) (all-substrates '(|RXN-17635|) ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|Protein-Arginine-Aminocarbinol|',\n", + " u'|PROTON|',\n", + " u'|Protein-Arginine-Imidazolidine|']" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "A list of reaction frames. \n", + "\"\"\"\n", + "\n", + "ecoli.all_substrates(rxns = ecoli.all_rxns(type = ':spontaneous')[0:1])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-cofactors\n", + "(all-cofactors )\n", + "(with-organism (:org-id '|ECOLI|) (all-cofactors ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|DIPYRROMETHANE|',\n", + " u'|GTP|',\n", + " u'|UBIQUINONE-8|',\n", + " u'|AMMONIUM|',\n", + " u'|LYS|',\n", + " u'|HEME_O|',\n", + " u'|CPD-18260|',\n", + " u'|PQQ|',\n", + " u'|SIROHEME|',\n", + " u'|Mo-molybdopterin-cofactor|']" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_cofactors()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-modulators\n", + "(all-modulators )\n", + "(with-organism (:org-id '|ECOLI|) (all-modulators ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|DEOXY-RIBOSE-1P|',\n", + " u'|CPD0-1546|',\n", + " u'|CPD0-1545|',\n", + " u'|NACL|',\n", + " u'|Gramicidins|',\n", + " u'|CPD0-1633|',\n", + " u'|G7642-MONOMER|',\n", + " u'|CPD-9229|',\n", + " u'|PENICILLIN|',\n", + " u'|CPD0-2358|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_modulators()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-transported-chemicals\n", + "(all-transported-chemicals :primary-only? nil)\n", + "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil))\n", + "all-transported-chemicals\n", + "(all-transported-chemicals :primary-only? t)\n", + "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? t))\n", + "all-transported-chemicals\n", + "(all-transported-chemicals :primary-only? nil :from-compartment '|CCO-CYTOSOL|)\n", + "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :from-compartment '|CCO-CYTOSOL|))\n", + "all-transported-chemicals\n", + "(all-transported-chemicals :primary-only? nil :to-compartment '|CCO-CYTOSOL|)\n", + "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :to-compartment '|CCO-CYTOSOL|))\n", + "all-transported-chemicals\n", + "(all-transported-chemicals :primary-only? nil :show-compartment 'cell)\n", + "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :show-compartment 'cell))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|LI+|',\n", + " u'|MELIBIOSE|',\n", + " u'|D-GALACTURONATE|',\n", + " u'|PROTON|',\n", + " u'|CPD0-2241|',\n", + " u'|GUANINE|',\n", + " u'|Nucleosides|',\n", + " u'|CPD-20888|',\n", + " u'|XANTHINE|',\n", + " u'|N-ACETYL-D-MANNOSAMINE-6P|']" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "from-compartment\n", + "Keyword, Optional The compartment that the chemical is coming from (see Cellular \n", + "Component Ontology). \n", + "to-compartment\n", + "Keyword, Optional The compartment that the chemical is going to (see Cellular \n", + "Component Ontology). \n", + "show-compartment\n", + "Keyword, Optional Show the form of the compound as it is present in the \n", + "specified compartment (see Cellular Component Ontology), if the compound is \n", + "modified during transport. \n", + "primary-only?\n", + "Keyword, Optional If true, filter out common transport compounds, such as \n", + "protons and Na+. \n", + "\"\"\"\n", + "\n", + "ecoli.all_transported_chemicals()[0:10]\n", + "ecoli.all_transported_chemicals(primary_only = True)[0:10]\n", + "ecoli.all_transported_chemicals(from_compartment = u'|CCO-CYTOSOL|')[0:10]\n", + "ecoli.all_transported_chemicals(to_compartment = u'|CCO-CYTOSOL|')[0:10]\n", + "ecoli.all_transported_chemicals(show_compartment = 'cell')[0:10] # not valid argument" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-protein-complexes\n", + "(all-protein-complexes :filter :all)\n", + "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n", + "all-protein-complexes\n", + "(all-protein-complexes :filter :hetero)\n", + "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :hetero))\n", + "all-protein-complexes\n", + "(all-protein-complexes :filter :homo)\n", + "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :homo))\n", + "all-protein-complexes\n", + "(all-protein-complexes :filter :all)\n", + "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|CPLX0-7660|',\n", + " u'|CPLX0-8247|',\n", + " u'|CPLX0-3102|',\n", + " u'|ACETYL-COA-CARBOXYLTRANSFER-CPLX|',\n", + " u'|CPLX0-7|',\n", + " u'|TRANS-CPLX-204|',\n", + " u'|FLAGELLAR-MOTOR-COMPLEX|',\n", + " u'|1-PFK|',\n", + " u'|CPLX0-8125|',\n", + " u'|CPLX0-7687|']" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "filter\n", + "Keyword The type of protein complexes to return. The argument must be one of the \n", + "following values:\n", + "\n", + ":all or t\n", + "Return all protein complexes. \n", + ":hetero\n", + "Return all heteromultimers. \n", + ":homo\n", + "Return all homomultimers. \n", + "\"\"\"\n", + "\n", + "ecoli.all_protein_complexes(filter = 'all')[0:10]\n", + "ecoli.all_protein_complexes(filter = 'hetero')[0:10]\n", + "ecoli.all_protein_complexes(filter = 'homo')[0:10]\n", + "ecoli.all_protein_complexes()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-transcription-factors\n", + "(all-transcription-factors :allow-modified-forms? t)\n", + "(with-organism (:org-id '|ECOLI|) (all-transcription-factors :allow-modified-forms? t))\n", + "all-transcription-factors\n", + "(all-transcription-factors :allow-modified-forms? t)\n", + "(with-organism (:org-id '|ECOLI|) (all-transcription-factors :allow-modified-forms? t))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|G6165-MONOMER|',\n", + " u'|PHOSPHO-NARP|',\n", + " u'|G6882-MONOMER|',\n", + " u'|MONOMER0-1|',\n", + " u'|G7947-MONOMER|',\n", + " u'|G6175-MONOMER|',\n", + " u'|EG11554-MONOMER|',\n", + " u'|PD01196|',\n", + " u'|EG10087-MONOMER|',\n", + " u'|EG10226-MONOMER|']" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "Side-Effects\n", + "\n", + "allow-modified-forms?\n", + "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", + "protein are returned. If false, then only unmodified forms of the proteins are \n", + "returned. The default value is t.\n", + "\"\"\"\n", + "\n", + "ecoli.all_transcription_factors()[0:10]\n", + "ecoli.all_transcription_factors(allow_modified_forms = True)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-genetic-regulation-proteins\n", + "(all-genetic-regulation-proteins :class '|Regulation| :allow-modified-forms? nil)\n", + "(with-organism (:org-id '|ECOLI|) (all-genetic-regulation-proteins :class '|Regulation| :allow-modified-forms? nil))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|G6165-MONOMER|',\n", + " u'|NARP-MONOMER|',\n", + " u'|TAR-CPLX|',\n", + " u'|G6882-MONOMER|',\n", + " u'|EG11140-MONOMER|',\n", + " u'|EG10881-MONOMER|',\n", + " u'|G7947-MONOMER|',\n", + " u'|G6175-MONOMER|',\n", + " u'|EG12111-MONOMER|',\n", + " u'|EG11554-MONOMER|']" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "class\n", + "Keyword, Optional The class |Regulation| or a subclass. It defaults to \n", + "|Regulation‑of‑Transcription‑Initiation|. \n", + "allow-modified forms?\n", + "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", + "protein are returned. If false, then only unmodified forms of the proteins are \n", + "returned. The default value is t.\n", + "\"\"\"\n", + "\n", + "ecoli.all_genetic_regulation_proteins(class_name = u'|Regulation|', allow_modified_forms = False)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-sigma-factors\n", + "(all-sigma-factors )\n", + "(with-organism (:org-id '|ECOLI|) (all-sigma-factors ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|EG11355-MONOMER|',\n", + " u'|RPOE-MONOMER|',\n", + " u'|RPOD-MONOMER|',\n", + " u'|RPON-MONOMER|',\n", + " u'|PD00440|',\n", + " u'|RPOS-MONOMER|',\n", + " u'|RPOH-MONOMER|']" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_sigma_factors()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-operons\n", + "(all-operons )\n", + "(with-organism (:org-id '|ECOLI|) (all-operons ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[[u'|TU0-8814|'],\n", + " [u'|TU0-8710|'],\n", + " [u'|TU0-13847|'],\n", + " [u'|TU0-13769|'],\n", + " [u'|TU0-13667|'],\n", + " [u'|TU00321|'],\n", + " [u'|TU0-13385|'],\n", + " [u'|TU00223|'],\n", + " [u'|TU0-14243|'],\n", + " [u'|TU0-14168|']]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_operons()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::enzyme )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::enzyme ))\n", + "rxns-w-isozymes\n", + "(rxns-w-isozymes :rxns '(|DCYSDESULF-RXN| |RXN-11837| |RXN-14142| |DIHYDROOROTATE-DEHYDROGENASE-RXN| |RXN-12402| |RXN0-5285| |GLUCOSE-1-PHOSPHAT-RXN| |INOSINE-NUCLEOSIDASE-RXN| |RXN0-6509| |RXN0-6575| |RXN0-7167| |GLYCOGENSYN-RXN| |PUTTRANSAM-RXN| |2.7.10.1-RXN| |5.99.1.2-RXN| |1.5.1.34-RXN| |DHDOGALDOL-RXN| |RXN-19777| |RXN0-1661| |RXN0-6975| |RXN0-5364| |RXN-12073| |RXN-14285| |RXN-18999| |RXN-17780| |GLUTRACE-RXN| |KETOACYLCOATHIOL-RXN| |3.1.13.5-RXN| |QUINOPRIBOTRANS-RXN| |RXN0-6734| |RXN0-7251| |RXN-11635| |DIHYDROXYMETVALDEHYDRAT-RXN| |3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN| |ACETOOHBUTREDUCTOISOM-RXN| |RXN0-5418| |RXN-2962| |RXN0-2161| |GLCNACPTRANS-RXN| |RXN-17796| |RXN-12508| |RXN-14478| |RXN-12816| |RIBOFLAVINSYNREDUC-RXN| |GLYCPDIESTER-RXN| |LTAA-RXN| |RXN0-6541| |DTMPKI-RXN| |RXN0-6980| |RXN0-961| |DALADEHYDROG-RXN| |GMP-SYN-NH3-RXN| |RXN0-6272| |3.1.22.4-RXN| |ACYLPHOSPHATASE-RXN| |2.1.1.79-RXN| |RXN-17920| |RXN0-2661| |RXN0-6998| |RXN-19381| |F16BDEPHOS-RXN| |GSPAMID-RXN| |MALTODEXGLUCOSID-RXN| |3.2.1.17-RXN| |FCLREDUCT-RXN| |RXN0-7007| |SERINE--TRNA-LIGASE-RXN| |RXN-11842| |RXN0-6459| |3.2.2.23-RXN| |AICARSYN-RXN| |RXN-18092| |FORMATEDEHYDROG-RXN| |RXN-7968| |RXN-18376| |RXN-8344| |RXN0-303| |GLUTAMIDOTRANS-RXN| |RXN-11484| |RXN-11396| |RXN-13202| |GALACTOACETYLTRAN-RXN| |H2PTEROATESYNTH-RXN| |METHYLMALONYL-COA-EPIM-RXN| |RXN0-6710| |RXN0-6506| |RXN0-7066| |SUCCINYLDIAMINOPIMTRANS-RXN| |FUCPALDOL-RXN| |GUANYLCYC-RXN| |1.5.1.20-RXN| |3.4.21.83-RXN| |ALLANTOINASE-RXN| |NADH-DEHYDROG-A-RXN| |2.7.7.8-RXN| |RXN-13403| |RXN-8992| |RXN0-3542| |RXN0-6485| |RXN0-703| |RXN-11633| |RXN-14073| |RXN0-4701| |GKI-RXN| |HOMSUCTRAN-RXN| |NADPYROPHOSPHAT-RXN| |1.1.1.39-RXN| |3.4.19.12-RXN| |RXN0-6532| |RXN0-7104| |THIAZOLSYN3-RXN| |RXN-12195| |2.1.1.77-RXN| |4.2.99.18-RXN| |ANTHRANSYN-RXN| |RXN-18709| |RXN-8675| |RXN-19362| |RXN0-1241| |RXN0-4121| |GLYCDEH-RXN| |RXN-11841| |RXN-14181| |RXN-15297| |RXN-11596| |RXN-14025| |CITLY-RXN| |GLURS-RXN| |ISOCHORSYN-RXN| |NUCLEOTIDE-PYROPHOSPHATASE-RXN| |RXN0-6948| |RXN0-6708| |RXN0-7187| |GDP-GLUCOSIDASE-RXN| |HOMOCYSMET-RXN| |2.7.7.60-RXN| |6PGLUCONOLACT-RXN| |ASPARTATE--TRNA-LIGASE-RXN| |3-PHOSPHOGLYCERATE-PHOSPHATASE-RXN| |RXN-19920| |RXN0-1863| |RXN0-5001| |RXN0-6526| |RXN0-7092| |RXN-14361| |RXN-15744| |GLYC3PDEHYDROGBIOSYN-RXN| |L-GLN-FRUCT-6-P-AMINOTRANS-RXN| |OXAMATE-CARBAMOYLTRANSFERASE-RXN| |2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN| |3PGAREARR-RXN| |RXN0-6945| |RXN0-7275| |TRYPSYN-RXN| |RXN-12587| |3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN| |ACETYLGLUTKIN-RXN| |BIS5-ADENOSYL-TRIPHOSPHATASE-RXN| |RXN-19312| |RXN-9951| |RXN-3641| |RXN0-2361| |RXN0-5074| |GLYOXIII-RXN| |RXN-12583| |RXN-14483| |RXN-16286| |RXN-11836| |RXN-14139| |GLYOXII-RXN| |LYSDECARBOX-RXN| |PGLYCDEHYDROG-RXN| |RXN-13158| |RXN0-6985| |RXN0-6984| |RXN0-985| |UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN| |GLUCOSAMINE-KINASE-RXN| |INOSINATE-NUCLEOSIDASE-RXN| |3.1.26.4-RXN| |ADENODEAMIN-RXN| |CHORISMATE-SYNTHASE-RXN| |3.1.26.5-RXN| |RXN-7632| |RXN0-2787| |RXN0-5127| |RXN0-6566| |RXN0-7166| |RXN-12886| |RXN-14524| |RXN-16689| |RXN-7682| |GTP-CYCLOHYDRO-II-RXN| |MANNONOXIDOREDUCT-RXN| |PHOSMANMUT-RXN| |2.7.1.148-RXN| |5.4.2.10-RXN| |RXN0-7013| 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"text": [ + "rxns-w-isozymes\n", + "(rxns-w-isozymes )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-w-isozymes ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|RXN-14142|',\n", + " u'|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " u'|2.7.10.1-RXN|',\n", + " u'|5.99.1.2-RXN|',\n", + " u'|1.5.1.34-RXN|',\n", + " u'|RXN-17780|',\n", + " u'|KETOACYLCOATHIOL-RXN|',\n", + " u'|RXN0-7251|',\n", + " u'|GLYCPDIESTER-RXN|',\n", + " u'|LTAA-RXN|']" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", + "result of (all‑rxns :enzyme).\n", + "\"\"\"\n", + "\n", + "ecoli.rxns_w_isozymes(rxns = ecoli.all_rxns(':enzyme'))[0:10]\n", + "ecoli.rxns_w_isozymes()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-rxns\n", + "(all-rxns ::enzyme )\n", + "(with-organism (:org-id '|ECOLI|) (all-rxns ::enzyme ))\n", + "rxns-catalyzed-by-complex\n", + "(rxns-catalyzed-by-complex :rxns '(|DCYSDESULF-RXN| |RXN-11837| |RXN-14142| |DIHYDROOROTATE-DEHYDROGENASE-RXN| |RXN-12402| |RXN0-5285| |GLUCOSE-1-PHOSPHAT-RXN| |INOSINE-NUCLEOSIDASE-RXN| |RXN0-6509| |RXN0-6575| |RXN0-7167| |GLYCOGENSYN-RXN| |PUTTRANSAM-RXN| |2.7.10.1-RXN| |5.99.1.2-RXN| |1.5.1.34-RXN| |DHDOGALDOL-RXN| |RXN-19777| |RXN0-1661| |RXN0-6975| |RXN0-5364| |RXN-12073| |RXN-14285| |RXN-18999| |RXN-17780| |GLUTRACE-RXN| |KETOACYLCOATHIOL-RXN| |3.1.13.5-RXN| |QUINOPRIBOTRANS-RXN| |RXN0-6734| |RXN0-7251| 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|XYLULOKIN-RXN| |RXN0-6373| |RXN0-7114| |THIKIN-RXN| |RXN-9528| |RXN0-5462| |4.3.1.15-RXN| |ARABISOM-RXN| |PYROXALTRANSAM-RXN| |RXN-9657| |CYTIKIN-RXN| |RXN0-1281| |RXN0-4181| |DIHYDLIPACETRANS-RXN| |RXN0-1139| |RXN-17848| |RXN-14188| |RXN-15298| |RXN0-5398| |RXN0-3341| |RXN0-5213| |ISOCIT-CLEAV-RXN| |O-SUCCHOMOSERLYASE-RXN| |RXN-17788| |RXN0-7299| |RIBULPEPIM-RXN| |RXN0-7188| |TRANS-RXN0-623| |RFFTRANS-RXN| |RXN-17391| |7-ALPHA-HYDROXYSTEROID-DEH-RXN| |ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| |DNA-DIRECTED-RNA-POLYMERASE-RXN| |2.3.1.41-RXN| |RXN-13163| |ENOYL-COA-HYDRAT-RXN| |RXN0-1882| |RXN0-5021| |RXN0-5507| |PRIBFAICARPISOM-RXN| |RXN-14363| |RXN-15761| |RXN0-6371| |L-IDONATE-2-DEHYDROGENASE-RXN| |P-PANTOCYSDECARB-RXN| |RNA-3-PHOSPHATE-CYCLASE-RXN| |DEHYDDEOXGALACTKIN-RXN| |RXN0-7280| |TRYPTOPHAN--TRNA-LIGASE-RXN| |ENTDB-RXN| |RXN-17955| |ACETYLORNDEACET-RXN| |BRANCHED-CHAINAMINOTRANSFERILEU-RXN| |RXN0-6381| |RXN0-5289| |RXN0-2381| |RXN0-5100| |RXN-17956| |RXN-17961| |RXN-14497| |RXN-16312| |RXN-17962| |LYSINE--TRNA-LIGASE-RXN| |PGLYCEROLTRANSI-RXN| |RXN-11313| |RXN-11277| |RXN0-986| |UDPNACETYLMURAMATEDEHYDROG-RXN| |FRUCTOKINASE-RXN| |PYRAMKIN-RXN| |ADENOSINE-NUCLEOSIDASE-RXN| |CHORISMATEMUT-RXN| |RXN0-6482| |RXN0-5264| |FPPSYN-RXN| |RXN0-279| |RXN0-5129| |1.1.1.271-RXN| |DHHB-METHYLTRANSFER-RXN| |RXN-14525| |RXN-16690| |RXN-18703| |PYRUVDEH-RXN| |RXN0-6481| |MANNOSE-ISOMERASE-RXN| |PHOSNACMURPENTATRANS-RXN| |RXN-11591| |RXN0-5375| |SORB6PDEHYDROG-RXN| |VALINE-PYRUVATE-AMINOTRANSFER-RXN| |GART-RXN| |1.1.1.264-RXN| |ALANINE--TRNA-LIGASE-RXN| |CYSTEINE-AMINOTRANSFERASE-RXN| |RXN0-6523| |RXN-17781| |RXN0-313| |RXN0-5199| |2-METHYLCITRATE-SYNTHASE-RXN| |RXN-18702| |RXN-17009| |RXN-19253| |R15-RXN| |MHPHYDROXY-RXN| |PPGPPSYN-RXN| |RXN-11833| |RXN-11589| |SULFITE-REDUCT-RXN| |DCDPKIN-RXN| |GLUCONOKIN-RXN| |RXN-12588| |DIMETHUROPORDEHYDROG-RXN| |ALTRODEHYDRAT-RXN| |RXN0-5228| |RXN0-6563| |GAPOXNPHOSPHN-RXN| |RXN0-3741| |2.6.1.57-RXN| |RXN-12894| |RXN0-5422| |PSERTRANSAM-RXN| |RXN-19630| |CARBPSYN-RXN| |RXN0-6522| |NAPHTHOATE-SYN-RXN| |DGDPKIN-RXN| |RXN-12002| |RXN-17797| |THREODEHYD-RXN| |RXN0-5329| |GLUTCYSLIG-RXN| |2-METHYLCITRATE-DEHYDRATASE-RXN| |ARGININE--TRNA-LIGASE-RXN| |RXN-17776| |RXN0-6727| |RIBOKIN-RXN| |RXN0-4281| |PYRUVFORMLY-RXN| |2TRANSKETO-RXN| |RXN-19249| |RXN-15341| |DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN| |RXN-2043| |DUDPKIN-RXN| |OHACYL-COA-DEHYDROG-RXN| |RXN0-5409| |RXN-12444| |RXN-11832| |TREHALA-RXN| |RXN-17792| |GLYCOLALD-DEHYDROG-RXN| |RXN0-7231| |RXN0-6274| |DLACTDEHYDROGFAD-RXN| |ATP-PYROPHOSPHATASE-RXN| |RIB5PISOM-RXN| |RXN0-6976| |GLUCONATE-5-DEHYDROGENASE-RXN| |RXN0-5051| |DTDPDEHYRHAMREDUCT-RXN| |3.1.21.1-RXN| |RXN-17930| |RXN0-6254| |RXN-6321| |RXN0-6511| |RXN0-6562| |PANTOATE-BETA-ALANINE-LIG-RXN| |RXN-10814| |RXN-11496| |TYROSINE-AMINOTRANSFERASE-RXN| |GPH-RXN| |2.5.1.64-RXN| |CARBOXYLATE-REDUCTASE-RXN| |ERYTHRON4PDEHYDROG-RXN| |RXN0-6999| |FADSYN-RXN| |RXN0-5108| |3.2.1.21-RXN| |RXN-19629| |RXN-16457| |RXN-18093| |RXN-8073| |RXN-10856| |URA-PHOSPH-RXN| |RXN-11397| |RXN-11867| |COBALADENOSYLTRANS-RXN| |FUCULOKIN-RXN| |H2NEOPTERINALDOL-RXN| |FGAMSYN-RXN| |RXN0-5146| |RXN0-6487| |RXN0-704| |GLUTATHIONE-SYN-RXN| |RXN-16788| |1.1.1.83-RXN| |3.4.21.102-RXN| |RXN0-6460| |PHOSPHOAMIDASE-RXN| |RXN-18710| |RXN-8770| |RXN0-6726| |XYLONATE-DEHYDRATASE-RXN| |RXN-11598| |RXN-14026| |RXN-18388| |CYTIDINEKIN-RXN| |GDPKIN-RXN| |HOMOCYSMETB12-RXN| |2PGADEHYDRAT-RXN| |RXN0-5210| |RXN0-6527| |RXN0-7100| |RXN-11573| |RXN-17330| |2-OCTAPRENYLPHENOL-HYDROX-RXN| |4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN| |RXN-19998| |PREPHENATEDEHYDROG-RXN| |RXN-9952| |GALACTOKIN-RXN|)))\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "rxns-catalyzed-by-complex\n", + "(rxns-catalyzed-by-complex )\n", + "(with-organism (:org-id '|ECOLI|) (rxns-catalyzed-by-complex ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|DCYSDESULF-RXN|',\n", + " u'|RXN-14142|',\n", + " u'|RXN-12402|',\n", + " u'|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " u'|PUTTRANSAM-RXN|',\n", + " u'|1.5.1.34-RXN|',\n", + " u'|DHDOGALDOL-RXN|',\n", + " u'|RXN-19777|',\n", + " u'|RXN-12073|',\n", + " u'|RXN-14285|']" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", + "result of (all‑rxns :enzyme).\n", + "\"\"\"\n", + "\n", + "ecoli.rxns_catalyzed_by_complex(rxns = ecoli.all_rxns(':enzyme'))[0:10]\n", + "ecoli.rxns_catalyzed_by_complex()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-enzymes\n", + "(all-enzymes )\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes ))\n", + "all-enzymes\n", + "(all-enzymes :type :any)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :any))\n", + "all-enzymes\n", + "(all-enzymes :type :chemical-change)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :chemical-change))\n", + "all-enzymes\n", + "(all-enzymes :type :small-molecule)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :small-molecule))\n", + "all-enzymes\n", + "(all-enzymes :type :transport)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :transport))\n", + "all-enzymes\n", + "(all-enzymes :type :non-transport)\n", + "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :non-transport))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|MHPELY-MONOMER|',\n", + " u'|G6571-MONOMER|',\n", + " u'|G7751-MONOMER|',\n", + " u'|G7910-MONOMER|',\n", + " u'|G6904-MONOMER|',\n", + " u'|PGLUCONDEHYDRAT-MONOMER|',\n", + " u'|MONOMER0-1241|',\n", + " u'|ACECITLY-CPLX|',\n", + " u'|G7422-MONOMER|',\n", + " u'|EG12069-MONOMER|']" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Keyword, Optional A type as taken from the argument to #'enzyme?. Defaults to \n", + ":chemical‑change.\n", + "\n", + ">> type\n", + "Optional Can take on one of the following values to select more precisely what \n", + "is meant by an “enzyme”:\n", + "\n", + ":any\n", + "Any protein that catalyzes a reaction is considered an enzyme. \n", + ":chemical-change\n", + "If the reactants and products of the catalyzed reactin differ, and not just by \n", + "their cellular location, then the protein is considered an enzyme. \n", + ":small-molecule\n", + "If the reactants of the catalyzed reaction differ and are small molecules, then \n", + "the protein is considered an enzyme. \n", + ":transport\n", + "If the protein catalyzes a transport reaction. \n", + ":non-transport\n", + "If the protein only catalyzes non-transport reactions. \n", + "\"\"\"\n", + "\n", + "ecoli.all_enzymes()[0:10]\n", + "ecoli.all_enzymes(type = ':any')[0:10]\n", + "ecoli.all_enzymes(type = ':chemical-change')[0:10]\n", + "ecoli.all_enzymes(type = ':small-molecule')[0:10]\n", + "ecoli.all_enzymes(type = ':transport')[0:10]\n", + "ecoli.all_enzymes(type = ':non-transport')[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "all-transporters\n", + "(all-transporters )\n", + "(with-organism (:org-id '|ECOLI|) (all-transporters ))\n" + ] + }, + { + "data": { + "text/plain": [ + "[u'|DCUA-MONOMER|',\n", + " u'|G7399-MONOMER|',\n", + " u'|YIDT-MONOMER|',\n", + " u'|CORA-MONOMER|',\n", + " u'|EG12134-MONOMER|',\n", + " u'|EG11486-MONOMER|',\n", + " u'|CYNX-MONOMER|',\n", + " u'|YJDL-MONOMER|',\n", + " u'|EG11512-MONOMER|',\n", + " u'|GLTP-MONOMER|']" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_transporters()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15rc1" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/pythoncyc/PGDB.py b/pythoncyc/PGDB.py index 469db75..356eed2 100644 --- a/pythoncyc/PGDB.py +++ b/pythoncyc/PGDB.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -22,3309 +22,3499 @@ import PTools import sys -import config +import config from PTools import PToolsError, PythonCycError from PToolsFrame import Symbol, PFrame, convertLispIdtoPythonId + if 'IPython' in sys.modules: - from IPython.display import display, HTML - -def may_be_frameid(x): - """ - This fn is useful to convert a string to a symbol - or a list of strings to a list of symbols, to make sure it is interpreted - as a frame id; but not to apply any conversion when the arg is not a string - or a list of strings. All functions of PGDB.py apply this fn on the - arguments that need a frame ids or PFrames. - - Parm - x: a Python object. - - Side Effect - Raise an error, if x is not None, String, PFrame, or a list of these. - - Returns - A symbol, list of symbols, or x unchanged. - """ - if x == None: - return None - elif isinstance(x,list): - return [may_be_frameid(y) for y in x] - if isinstance(x,PFrame): - return x - elif isinstance(x,basestring): - return Symbol(x) - else: raise PythonCycError('Error: the argument must a string or a PFrame but given {0}.'.format(x)) - - -def mkey(s): - """ - A simple function to convert a string into a Lisp keyword. - - Parm - s, any Python object - Returns - if s is a string, it is suffixed by ':', otherwise s itself. - """ - if isinstance(s,basestring): - return ':'+s - else: return s + from IPython.display import display, HTML + +def may_be_frameid(obj): + """ + This fn is useful to convert a string to a symbol or a list of strings to a list + of symbols, to make sure it is interpreted as a frame id; but not to apply any + conversion when the arg is not a string or a list of strings. All functions of + PGDB.py apply this fn on the arguments that need a frame ids or PFrames. + + Parm + obj, any Python object. + + Side Effect + Raise an error if obj is not None, String, PFrame, or a list of these. + + Returns + A symbol, list of symbols, or obj unchanged. + """ + if obj == None: + return None + elif isinstance(obj, list): + return [ may_be_frameid(y) for y in obj ] + elif isinstance(obj, PFrame): + return obj + elif isinstance(obj, basestring): + return Symbol(obj) + else: + raise PythonCycError('Error: the argument must a string or a PFrame, but given {0}.'.format(x)) + +def mkey(obj): + """ + A simple function to convert a string into a Lisp keyword. + + Parm + obj, any Python object + + Returns + if obj is a string, it is suffixed by ':', otherwise obj itself. + """ + if isinstance(obj, basestring): + return ':' + obj + else: + return obj def convertArgToLisp(arg, inquote=False): - """ - Convert the arg into an acceptable quoted object for Python server - running on Pathway Tools. Note that any list is converted to - a quoted Lisp list. - - Parm - arg, a PFrame, a string, a number, a boolean, None or an s-expr. - inquote, a Boolean, True => this arg is inside an already quoted expression. - Return - a string, the arg is transformed to be acceptable for the Python Lisp server. - """ - if isinstance(arg, Symbol): - return ("" if inquote else "'")+arg._name - # Type basestring includes string and unicode string. - elif isinstance(arg, basestring): - # It is either a symbol, a string or a keyword. - # If it starts and ends with '|', assumes it is a symbol and add - # a quote if not already in a quoted context otherwise just - # translates to a string. - # The tests for symbols and keywords are simplified - # because if a tab or any characters not representing a Lisp - # keyword or symbols is embedded in the string, it is not detected. - if arg[0] == '|' and arg[-1] == '|' and not (' ' in arg): - return ("" if inquote else "'")+arg - elif arg[0] == ':' and not (' ' in arg): - return arg - else: return '"'+arg+'"' - # Note: False and True are also of type int. - # So, do this test before isinstance(... (int)) - elif isinstance(arg, bool): - return 't' if arg else 'nil' - elif arg == None: - return 'nil' - elif isinstance(arg, (int, long, float, complex)): - return str(arg) - elif isinstance(arg, PFrame): - # Just using the frameid is enough (there is no need to - # refer to the PGDB) because the arg is used in a call - # using the macro 'with-organism' where the PGDB is specified. - return arg.frameid - elif isinstance(arg, list): - return (("" if inquote else "'") + - '('+' '.join(convertArgToLisp(e,inquote=True) for e in arg) + ')') - elif isinstance(arg, dict): - # Convert a dictionary into a list of lists. - # {'a':2, 'b':3} => (('a' . 2) ('b' . 3)) - return convertArgToLisp(dict.items(arg)) - elif isinstance(arg, tuple): - # A Python tuple becomes an improper list in Lisp - # (1,) => (NIL . 1) - # (1,2) => (1 . 2) - # (1,2,3) => (1 2 . 3) - return (("" if inquote else "'") + - '('+(' '.join(convertArgToLisp(e,inquote=True) for e in arg[0:-1]) if (len(arg)>1) else '()') + ' . ' - + convertArgToLisp(arg[-1],inquote=True) + ')') - else: raise PythonCycError('PythonCyc does not know how to convert to Lisp the Python argument {0}.'.format(arg)) + """ + Convert arg into an acceptable quoted object for Python server running on + Pathway Tools. Note that any list is converted to a quoted Lisp list. + + Parm + arg + a PFrame, a string, a number, a boolean, None or an s-expr. + inquote + a Boolean, True means arg is inside an already quoted expression. + + Return + a string, the arg is transformed to be acceptable for the Python Lisp server. + """ + if isinstance(arg, Symbol): + return ("" if inquote else "'") + arg._name + + # Type basestring includes string and unicode string. + elif isinstance(arg, basestring): + # It is either a symbol, a string or a keyword. + # If it starts and ends with '|', assumes it is a symbol and add + # a quote if not already in a quoted context otherwise just + # translates to a string. + # The tests for symbols and keywords are simplified + # because if a tab or any characters not representing a Lisp + # keyword or symbols is embedded in the string, it is not detected. + if arg[0] == '|' and arg[-1] == '|' and not (' ' in arg): + return ("" if inquote else "'") + arg + elif arg[0] == ':' and not (' ' in arg): + return arg + else: + return '"' + arg + '"' + + # Note: False and True are also of type int. + # So, do this test before isinstance(... (int)) + elif isinstance(arg, bool): + return 't' if arg else 'nil' + elif arg == None: + return 'nil' + elif isinstance(arg, (int, long, float, complex)): + return str(arg) + elif isinstance(arg, PFrame): + # Just using the frameid is enough (there is no need to + # refer to the PGDB) because the arg is used in a call + # using the macro 'with-organism' where the PGDB is specified. + return arg.frameid + elif isinstance(arg, list): + return (("" if inquote else "'") + + '('+' '.join(convertArgToLisp(e, inquote=True) for e in arg) + ')') + elif isinstance(arg, dict): + # Convert a dictionary into a list of lists. + # {'a':2, 'b':3} => (('a' . 2) ('b' . 3)) + return convertArgToLisp(dict.items(arg)) + elif isinstance(arg, tuple): + # A Python tuple becomes an improper list in Lisp + # (1,) => (NIL . 1) + # (1,2) => (1 . 2) + # (1,2,3) => (1 2 . 3) + return (("" if inquote else "'") + + '(' + (' '.join(convertArgToLisp(e, inquote=True) for e in arg[0:-1]) if (len(arg) > 1) else '()') + ' . ' + + convertArgToLisp(arg[-1], inquote=True) + ')') + else: + raise PythonCycError('PythonCyc does not know how to convert to Lisp the Python argument {0}.'.format(arg)) def prepareFnCall(fn, *args, **kwargs): - """ - Prepare all arguments and keyword arguments for a function call to Pathway Tools. - Parms - fn, a string, the name of the Lisp function to call. - args, list of arguments - kwargs, list of keyword arguments - Return - a string which represents a Lisp fn call with args and keyword args. - """ - args2 = ' '.join([convertArgToLisp(arg) for arg in args]) - keywords = ' '.join([':'+key+' '+str(convertArgToLisp(kwargs[key])) - for key in kwargs if kwargs[key] != None]) - return '('+fn+' '+args2+' '+keywords+')' - + """ + Prepare all arguments and keyword arguments for a function call to Pathway Tools. + + Parms + fn + a string, the name of the Lisp function to call. + args + list of arguments + kwargs + list of keyword arguments + + Return + a string which represents a Lisp fn call with args and keyword args. + """ + args2 = ' '.join([convertArgToLisp(arg) for arg in args]) + keywords = ' '.join([ ':' + key + ' ' + str(convertArgToLisp(kwargs[key])) + for key in kwargs if kwargs[key] != None ]) + + lisp_query = '(' + fn + ' ' + args2 + ' ' + keywords + ')' + print lisp_query + return lisp_query class PGDB(): - """ - Please consult the the tutorial.html file under the doc directory - for an introduction on how to use this class. - - """ - - def __init__(self, orgid): - """ - Once a PGDB object is created, it has been validated that the - organism (orgid) exists on the running Pathway Tools server. - From that PGDB object (e.g. ecoli), many classes of objects - can be retrieved by using the attribute syntax of Python, such - as ecoli.reactions. - """ - if config._debug: - print "PGDB __init__" - self._orgid = "unknown" - self._error = False - # All PFrame objects of the PGDB are stored in attribute _frames, keyed by their frame ids. - self._frames = {} - # Verify that the running Pathway Tools has the PGDB (organism). - try: - r = PTools.sendQueryToPTools('(orgid-exist-p \''+orgid+')') - except PToolsError, msg: - raise PythonCycError('Pathway Tools was unable to verify if organism (orgid) %s is known in your running Pathway Tools. More specifically: %s' % (orgid, msg)) - if not r: - raise PythonCycError("The organism orgid %s is unknown. Use pythoncyc.all_orgids() to get a list of known orgids." % orgid) - self._error = True - else: - self._orgid = orgid - return None - - def __getinitargs__(self): - """ For the Pickle module. """ - return (self._orgid,) - - def __getstate__(self): - """ For the Pickel module """ - return self.__dict__.copy() - - def __setstate__(self, dict): - """ For the Pickel module """ - self.__dict__ = dict - - def __repr__(self): - return self.__str__() - - def __str__(self): - return '' - - def __dir__(self): - return (dir(self.__class__) + self.__dict__.keys()) - - def _nb_pframes(self): - """ - Return the number of PFrame objects accessible as attributes for a PGDB object. - """ - return len(self._frames) - - def __setattr__(self, attr, val): - if attr.startswith('_'): - self.__dict__[attr] = val - return None - attrId = convertLispIdtoPythonId(attr) - if isinstance(val, PFrame): - self._frames[attrId] = val - else: - self.__dict__[attrId] = val - return None - - def __getattr__(self, attr): - """ - Attributes for a PGDB may refer to frame ids. A frame id that - has dashes in Pathway Tools, is converted to attribute with - underscores '_' instead. If an attribute does not exist yet, - a request to Pathway Tools is done to verify if it may exist - as an instance or as a class. PFrame instances and classes are - created automatically when the corresponding instances or - classes exist in the PGDB. - """ - if config._debug: - print "PGDB ",self._orgid, "__getattr__", attr - # If the converted attribute exists as an attribute. - attrId = convertLispIdtoPythonId(attr) - if attrId in self.__dict__: - return self.__dict__[attrId] - if isinstance(attr,int): - return self._frames[attr] - if attrId in self._frames: - return self._frames[attrId] - # It could be an access to a class of objects (e.g. genes -> |Genes|). - realClassName = self.is_a_class_name(attr) - if realClassName: - # Use realClassName for the frame id, not attr. - return self.get_class_data(realClassName) - # It could be an instance in the PGDB. Try to create a frame for it. - realInstanceName = self.is_an_instance_name(attr) - if realInstanceName: - # Use the realname for the frame-id so that retrieving the - # object from Pathway Tools will work. - f = PFrame(realInstanceName, self, getFrameData=True, isClass=False) - return f - else: - return None - - if 'IPython' in sys.modules: - def _ipython_display_(self): - table = "" - # A PGDB frame may contain thousands of attributes, one - # for each instance. This output is too large to print in - # most cases. Print a succinct representation of the PGDB frame. - table = table+"" - table = table+"" - table = table+"
orgid"+self._orgid+"
Number of PFrames"+str(self._nb_pframes())+"
" - display(HTML(table)) - - def __setitem__(self, attr, val): - attrId = convertLispIdtoPythonId(attr) - if isinstance(val, PFrame): - self._frames[attrId] = val - else: - self.__dict__[attrId] = val - return None - - def __getitem__(self, index): - if config._debug: - print "PGDB __getitem__", index - if (isinstance(index,int) or isinstance(index,slice)) : - if self._frames: - return self._frames[index] - else: - raise PythonCycError('This PGDB has no _frames attribute.') - - # Accessing an item such as ecoli['trp'], index is a string not a number. - if index in self._frames: - return self._frames[index] - else: - attrId = convertLispIdtoPythonId(index) - if attrId in self._frames: - return self._frames[attrId] - else: - return self.__getattr__(index) - - def __eq__(self, other): - # The name of the orgid determines the object. - if isinstance(other, PGDB): - return self._orgid == other._orgid - else: - return False - - def __ne__(self, o): - return not self.__eq__(o) - - def save_pgdb(self): - """ - Save a PGDB that has been modified in the running Pathway Tools server. - The PGDB that will be saved is based on the orgid of this PGDB object. - """ - return self.sendPgdbFnCallBool('save-kb') - - def get_major_classes(self): - """ - Get from Pathway Tools the classes Reactions, Pathways, Genes, - Compounds, Proteins, and all their instances with their data. - This method is very time consuming has - several ten of thousands of frames need to be transferred - from Pathway Tools and the corresponding PFrames need to be created. - """ - self.reactions - self.pathways - self.genes - self.compounds - self.proteins - self.get_frame_objects([f.frameid for f in self.reactions.instances]) - self.get_frame_objects([f.frameid for f in self.pathways.instances]) - self.get_frame_objects([f.frameid for f in self.genes.instances]) - self.get_frame_objects([f.frameid for f in self.compounds.instances]) - self.get_frame_objects([f.frameid for f in self.proteins.instances]) - - def sendPgdbQuery(self, query): - """ - Send a query for a specific PGDB using its orgid. - Use the macro with-organism for the Lisp Python server. - - Parm - query, a string. That string should be acceptable to the Lisp Python server. - Return - the result (as a Python object) of the execution of the query in Pathway Tools. - """ - # Evaluate a query in the context of this PGDB. - if self._orgid == "unknown": - print "Cannot send any query because the selected organism is unknown." - return None - else: - return PTools.sendQueryToPTools('(with-organism (:org-id \''+self._orgid+') '+query+')') - - def sendPgdbFnCallBool(self, fn, *args, **kwargs): - """ - Send a PGDB query to Pathway Tools that will return a Bool value. - This method takes care of translating no value or an empty list to False. - """ - result = self.sendPgdbFnCall(fn, *args, **kwargs) - if result == None or result == []: - return False - else: return result - - def sendPgdbFnCallList(self, fn, *args, **kwargs): - """ - Send a PGDB query to Pathway Tools that will return a List value. - This method takes care of translating no value or False to an empty list. - """ - result = self.sendPgdbFnCall(fn, *args, **kwargs) - if result == None or result == False: - return [] - else: return result - - def sendPgdbFnCall(self, fn, *args, **kwargs): - """ - Send a PGDB query to Pathway Tools based on function fn and arguments args and - kwargs (keyword args) and return the result. If multiple values are - returned by fn, the Pathway Tools Python server transforms them into a list. - """ - fnCall = prepareFnCall(fn, *args, **kwargs) - return self.sendPgdbQuery(fnCall) - - def is_a_class_name(self, className): - """ - Verify that className is a known class in Pathway Tools. - Return the real name of that class because the className may have - been transformed by fn class-name-p to generate the closest real class name. - - Parm - className, a string, the class name to verify. - Return - a string, either className itself, or modified by replacing - '_' to '-' or some case letters changed to match an existing class - name in Pathway Tools. - """ - return self.sendPgdbFnCallBool('class-name-p', className) - - def get_class_data(self, realClassName, getInstancesData=False): - """ - Retrieve the class slots and their values, creating a PFrame for the class. - Retrieve also the list of instances from Pathway Tools and - create a PFrame for each instance. Store the list of PFrames - in attribute 'instances' of the class object. If getInstancesData is True, - get also all instances slots and their data. - - Parms - realClassName, a string, the real name of the class to retrieve. - getInstancesData, boolean, True => get the slots and data of all instances. - - Returns - A PFrame representing the class with all its slot names - as Python attributes. - """ - fclass = PFrame(realClassName, self, getFrameData=True, isClass = True) - attrId = convertLispIdtoPythonId(realClassName) - frameids = self.sendPgdbFnCallList('get-class', fclass) - if not (frameids == None): - if getInstancesData: - # Create PFrame instances with all their slots and data. - instances = self.get_frame_objects(frameids) - else: - # Create PFrame instances but the data for each frame is not brought in now. - # Reuse a PFrame for a frameid, if it already exists for this PGDB. - instances = self.create_frame_objects(frameids) - fclass.__dict__['instances'] = instances - return fclass - - def create_frame_objects(self, frameids): - """ - Create all the required PFrames for the given frameids. - If a PFrame already exist for a frameid on the PGDB, reuse - that PFrame, otherwise create a PFrame. No data is transferred - from Pathway Tools. - - Parm - frameids, list of frame ids (strings) - Side-Effects - self is modified to contain new PFrames indexed on new frameids - Return - list of PFrames - """ - pframes = [] - for frameid in frameids: - attrID = convertLispIdtoPythonId(frameid) - if attrID in self.__dict__: - f = self.__dict__[attrID] - else: - f = PFrame(frameid, self) - self.__dict__[attrID] = f - pframes.append(f) - return pframes - - def get_frame_objects(self, frameids): - """ - For each frame id of the list frameids, retrieve the slots - and their data. Reuse the PFrame of frameid if it already exist for this PGDB, - otherwise create one and attach it to this PGDB. - - Parm - frameids, list of frame ids (strings). - Return - list of PFrames, one for each frame id. - """ - frameObjects = self.sendPgdbFnCallList('get-frame-objects', may_be_frameid(frameids)) - pframes = [] - for frameid, slotsData in frameObjects.iteritems(): - attrID = convertLispIdtoPythonId(frameid) - if attrID in self.__dict__: - f = self.__dict__[attrID] - else: - f = PFrame(frameid, self) - self.__dict__[attrID] = f - pframes.append(f) - f._gotframe = True - for slot, data in slotsData.iteritems(): - f.__dict__[convertLispIdtoPythonId(slot)] = data - return pframes - - def is_an_instance_name(self, frameid): - """ - Similar to method is_a_class_name but for a frame that is not a class. - If frameid is a real frame id of an object of this PGDB, returns frameid as is. - If not, try to convert frameid to an exist frame id by transforming cases of - letters and underscores to dashes in frameid. - - Parm - frameid, a string. - - Returns - a string representing an existing frame id in the PGDB. - """ - return self.sendPgdbFnCallBool('frameid-instance-p', Symbol(frameid)) - - def get_class_all_instances(self, className): - """ - Get all instances of the given class name for this PGDB. - ClassName must be exactly as Pathway Tools expect the name of the class, - no conversion is applied. - - Parm - className, a symbol specified as a string (e.g., '|Reactions|') - - Returns - list of frameids - """ - return self.sendPgdbFnCallList('gcai', Symbol(className)) - - def get_class_all_subs(self, classArg): - """ - Get all subclasses of the given class name for this PGDB. - If classArg is a string, it must be exactly as Pathway Tools expect the name of the class, - no conversion is applied. - - Parm - classArg, a symbol specified as a string (e.g., '|Reactions|') or as - a PFrame. - - Returns - list of frameids corresponding to the subclasses of the classArg. - """ - return self.sendPgdbFnCallList('get-class-all-subs', classArg) - - def run_fba(self, fileName): - """ - In PythonCyc there is a run_fba method defined globally in the pythoncyc - module and there is this version which is run under a specific PGDB. - Notice though that the FBA input file provided will decide which organism - is used for running FBA and may override this PGDB. - - Parms - fileName, a string which is the name of the FBA input file on the - running Pathway Tools machine. - - Returns - A list with the following values: - 1) True <=> success, the FBA completed without error (for growth, see 5) - 2) List of error messages, if any - 3) List of output messages generated by MetaFlux (FBA module) during parsing - and execution - 4) The solver (SCIP) status symbol - 5) The flux of the objective biomass, non-zero if growth - 6) Number of growth cases if FBA input file is a knockout run, - or the number of active reactions if the FBA input file is solving a model - 7) The list of reactions that were in the model after instantiation - 8) The list of reactions that were active (non zero flux) with their fluxes - """ - return self.sendPgdbFnCall('python-run-fba', fileName) - - def get_slot_values(self, frameid, slotName): - """ - Return the slot values of a frame object. - Parms - frameid - a string representing the unique identifier for a frame object. - slotName - a string representing the slot of the frame object. - - Returns - list of values of the given slot. Values can be frameids, booleans, - strings, or numbers. - - Example: - To get the substrates participating on the left of reaction RXN-9000: - meta.get_slot_values('RXN-9000', 'LEFT') - where meta is a variable bound to a PGDB object. - """ - return self.sendPgdbFnCallList('get-slot-values', Symbol(frameid), Symbol(slotName)) - - def put_slot_values(self, frameid, slotName, val): - """ - Modify the slot values of a frame object with the given val. Val is typically - a list of objects. - - Important: The modified frame is not updated for any PFrame object that might has been - previously loaded from that PGDB. This operation should be used only - for its effect on the PGDB in the running Pathway Tools application. - Parms - frameid - a string representing the unique identifier for a frame object. - slotName - a string representing the slot of the frame object. - val - a value to store in the slot, typically a list of values or objects. - Side-Effects - The slot of that frame is replaced with the new value. - - Returns - Nothing - Example: - To put the substrates participating on the left of reaction RXN-9000: - put_slot_values('RXN-9000', 'LEFT', ['CPD-9459','CPD-9460']) - """ - return self.sendPgdbFnCallList('put-slot-values', Symbol(frameid), Symbol(slotName), val) - - def put_slot_value(self, frameid, slotName, val): - """ - Modify the slot value of a frame object with the given val. Val is a single - value (e.g., not a list). - - Important: The modified frame is not updated for any PFrame object that might has been - previously loaded from that PGDB. This operation should be used only - for its effect on the PGDB in the running Pathway Tools application. - - Parms - frameid - a string representing the unique identifier for a frame object. - slotName - a string representing the slot of the frame object. - val - a value to store in the slot. - - Side-Effects - The slot of that frame is replaced with the new value - - Returns - Nothing - Example: - To put the Gibbs free energy of reaction RXN-9000: - put_slot_value('RXN-9000', 'GIBBS-0', 7.52) - """ - return self.sendPgdbFnCall('put-slot-value', Symbol(frameid), Symbol(slotName), val) - - def get_slot_value(self, frameid, slotName): - """ - Return the single slot value of a frame object. - Parms - frameid - a string representing the unique identifier for a frame object. - slotName - a string representing the slot of the frame object. - Example: - To get the substrates participating on the left of reaction RXN-9000: - get_slot_values('RXN-9000', 'LEFT') - """ - return self.sendPgdbFnCall('get-slot-value', Symbol(frameid), Symbol(slotName)) - - def all_pathways(self, selector='all', base=False): - """ - Description - Returns a list of pathway instance frames of a specified type. - Parms - selector - Selects whether all pathways, or just - small-molecule metabolism base pathways. Can take either - 'all' or 'small-molecule'. Defaults to 'all'. - base - If this boolean parameter is True, only includes - base pathways. Otherwise, all pathways, including - superpathways, will be returned. - - Return value - A list of instances of class Pathways. - """ - return self.sendPgdbFnCallList('all-pathways', mkey(selector), base) - - def all_reactions(self, type='metab-smm'): - return self.all_rxns(type) - - def all_rxns(self, type='metab-smm'): - """ - Description - Returns a set of reactions that fall within a particular category. - Parms - type - The type of reaction to return. Defaults to - 'metab-smm'. The possible values are: - - 'all' - All reactions. - 'metab-pathways' - All reactions found within metabolic pathways. Includes - reactions that are pathway holes. May include a handfull - of reactions whose substrates are macromolecules, e.g., - ACP. Excludes transport reactions. - 'metab-smm' - All reactions of small molecule metabolism, whether or - not they are present in a pathway. Subsumes - metab-pathways. - 'metab-all' - All enzyme-catalyzed reactions. Subsumes metab-smm. - 'enzyme' - All enzyme-catalyzed reactions (i.e., instances of - either EC-Reactions class or Unclassified-Reactions class). - 'transport' - All transport reactions. - 'small-molecule' - All reactions whose substrates are all small molecules, - as opposed to macromolecules. Excludes transport reactions. - 'protein-small-molecule-reaction' - One of the substrates of the reaction is a - macromolecule, and one of the substrates of the reaction - is a small molecule. - 'protein-reaction' - All substrates of the reaction are proteins. - 'trna-reaction' - One of the substrates of the reaction is a tRNA. - 'spontaneous' - Spontaneous reactions. - 'non-spontaneous' - Non-spontaneous reactions that are likely to be enzyme - catalyzed. Some reactions will be returned for type - non-spontaneous that will not be returned by enzyme. - - Return value - A list of reaction frame ids. - """ - return self.sendPgdbFnCallList('all-rxns', mkey(type)) - - def all_substrates(self, rxns): - """ - Description - Returns all unique substrates used in the reactions specified by - the parameter rxns. - Parms - rxns - A list of reaction PFrames or frame ids. - - Return value - A list of compound frame ids. There might be strings in the list, - as the left and right slots of a reaction frame can - contain strings. - """ - return self.sendPgdbFnCallList('all-substrates', may_be_frameid(rxns)) - - def all_cofactors(self): - """ - Description - Return a list of all cofactors used in the current PGDB. - Parms - None. - - Return value - A list of cofactor frame ids. - """ - return self.sendPgdbFnCallList('all-cofactors') - - - def all_modulators(self): - """ - Description - Enumerate all of the modulators, or direct regulators, in the - current PGDB. - Parms - None. - - Return value - A list of regulator frame ids. - """ - return self.sendPgdbFnCallList('all-modulators') - - - def all_sigma_factors(self): - """ - Description - Enumerate all RNA polymerase sigma factors. - Parms - None. - - Return value - A list of all instances of the class Sigma-Factors. - """ - return self.sendPgdbFnCallList('all-sigma-factors') - - def all_operons(self): - """ - Description - Enumerates all operons. In this case, an operon is defined as a - list of overlapping instances of Transcription-Units. - Parms - None. - - Return value - A list of lists of Transcription-Units, where all - Transcription-Units in the list belong to the same operon. - """ - return self.sendPgdbFnCallList('all-operons') - - def all_transporters(self): - """ - Description - Enumerate all transport proteins. - Parms - None. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('all-transporters') - - def all_transported_chemicals(self, from_compartment=None, to_compartment=None, primary_only=False): - """ - Description - Enumerates all chemicals transported by transport reactions in - the current PGDB. - Parms - - from_compartment - Keyword, The compartment that the chemical is - coming from (see Cellular Component Ontology). - to_compartment - Keyword, The compartment that the chemical is - going to (see Cellular Component Ontology). - primary_only - Keyword, If True, filter out common transport - compounds, such as protons and Na+. - - Return value - A list of compound frame ids. - """ - kwargs = {'from-compartment': may_be_frameid(from_compartment), - 'to-compartment': may_be_frameid(to_compartment), - 'primary-only?': primary_only} - return self.sendPgdbFnCallList('all-transported-chemicals', **kwargs) - - def all_protein_complexes(self, filter='all'): - """ - Description - Enumerates different types of protein complexes. - Parms - filter - Keyword, The type of protein complexes to return. The - argument must be one of the following values: - - 'all' - Return all protein complexes. - 'hetero' - Return all heteromultimers. - 'homo' - Return all homomultimers. - - Return value - A list of protein complex frame ids. - """ - kwargs = {'filter': mkey(filter)} - return self.sendPgdbFnCallList('all-protein-complexes', **kwargs) - - def all_transcription_factors(self, allow_modified_forms=True): - """ - Description - Enumerates all transcription factors, or just unmodified forms - of transcription factors. - Parms - allow_modified_forms - Keyword, A boolean value. If True, modified and - unmodified forms of the protein are returned. If false, then - only unmodified forms of the proteins are returned. The - default value is t. - - Return value - A list of protein frame ids that are transcription factors. - """ - kwargs = {'allow-modified-forms?': allow_modified_forms} - return self.sendPgdbFnCallList('all-transcription-factors', **kwargs) - - def all_genetic_regulation_proteins(self, allow_modified_forms=True, class_name=None): - """ - Description - Enumerates all proteins that are involved in genetic regulation - of a particular given class. Optionally, just unmodified forms - of the proteins are returned. - Parms - class_name - Keyword, The class Regulation or a subclass. - It defaults to Regulation-of-Transcription-Initiation. - allow_modified_forms - Keyword, A boolean value. If True, modified and - unmodified forms of the protein are returned. If false, then - only unmodified forms of the proteins are returned. The - default value is True. - - Return value - A list of protein frames that are involved in the specified form - of regulation. - """ - kwargs = {'allow-modified-forms?': allow_modified_forms, - 'class' : Symbol(class_name)} - return self.sendPgdbFnCallList('all-genetic-regulation-proteins', **kwargs) - - - def rxns_w_isozymes(self, rxns=None): - """ - Description - Enumerate all reactions that have isozymes (distinct proteins or - protein classes that catalyze the same reaction). - Parms - rxns - Keyword, A list of instances of the class - Reactions. Defaults to the result of (all-rxns :enzyme). - - Return value - A list of A list of instances of the class Reactions with - isozymes. - """ - kwargs = {'rxns': may_be_frameid(rxns)} - return self.sendPgdbFnCallList('rxns-w-isozymes', **kwargs) - - def rxns_catalyzed_by_complex(self, rxns=None): - """ - Description - Enumerates all reactions catalyzed by an enzyme that is a - protein complex. - Parms - rxns - Keyword, A list of instances of the class - Reactions. Defaults to the result of (all-rxns :enzyme). - - Return value - A list of instances of the class Reactions with a protein - complex as an enzyme. - """ - kwargs = {'rxns': may_be_frameid(rxns)} - return self.sendPgdbFnCallList('rxns-catalyzed-by-complex', **kwargs) - - def all_enzymes(self, type=None): - """ - Description - Return all enzymes of a given type. - Parms - type - Keyword, A type as taken from the parameter to - fn enzyme. Defaults to 'chemical-change'. - - Return value - A list of instances of class Proteins. - """ - kwargs = {'type': type} - return self.sendPgdbFnCallList('all-enzymes', **kwargs) - - - def genes_of_reaction(self, rxn): - """ - Description - Return all genes that encode the enzymes of a given reaction. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('genes-of-reaction', may_be_frameid(rxn)) - - def substrates_of_reaction(self, rxn): - """ - Description - Return all of the reactants and products of a given reaction. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - - Return value - A list that may consist of children of class Compounds, - children of class Polymer-Segments, or strings. - """ - return self.sendPgdbFnCallList('substrates-of-reaction', may_be_frameid(rxn)) - - def enzymes_of_reaction(self, rxn, species=None, experimental_only=None, local_only=None): - """ - Description - Return the enzymes that catalyze a given reaction. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - species - Keyword, A list of species, such that in a - multi-organism PGDB such as MetaCyc, only proteins found in - those organisms will be returned. This list can include - valid org-ids, children of class Organisms, and - strings. Please see the documentation for the species - slot-unit for more information. Default value is nil. - experimental_only - Keyword, When True, only return enzymes that have - a non-computational evidence code associated with it. - local_only - Keyword, When True, only return enzymes that - catalyze the specific form of the reaction, as opposed to - enzymes that are known to catalyze a more general form - (i.e., class) of the reaction. - - Return value - A list of children of class Proteins or class - Protein-RNA-Complexes. - """ - kwargs = {'species': species, - 'experimental-only?': experimental_only, - 'local-only-p': local_only} - return self.sendPgdbFnCallList('enzymes-of-reaction', may_be_frameid(rxn), **kwargs) - - def reaction_reactants_and_products(self, rxn, direction=None, pwy=None): - """ - Description - Return the reactants and products of a reaction, based on a - specified direction. The direction can be specified explicity or - by giving a pathway as an argument. It is an error to both - specify the pathway and the explicit direction. If neither an - explicit direction or a pathway is given as an argument, then - the direction is computationally inferred from available - evidence within the PGDB. - Parms - rxn - An instance of the class Reactions, that is, a frame id or PFrame. - direction - Keyword, Can take on the following values: - - 'L2R' - The reaction direction goes from 'left to right', as - described in the Reactions instance. - 'R2L' - The reaction direction goes from 'right to left'; the - opposite of what is described in the Reactions - instance. - - pwy - Keyword, An instance of the class Pathways, a frame id or PFrame. - - Return value - Returns multiple values as a list. The first value is a list of reactants - as determined by the direction of the reaction, and the second - value is a list of the products as determined by the direction - of the reaction. Both lists have items that are children of - class Compounds, children of class Polymer-Segments, or - strings. - """ - kwargs = {'direction': direction, 'pwy': may_be_frameid(pwy)} - return self.sendPgdbFnCall('reaction-reactants-and-products', may_be_frameid(rxn), **kwargs) - - def reaction_type(self, rxn): - """ - Description - Returns a keyword describing the type of reaction. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - - Return value - A string from the following list: - - 'small-molecule' - All substrates are small molecules, or small-molecule classes. - 'transport' - A substrate is marked with different compartment annotations - in the left and right slots. - 'protein-small-molecule-reaction' - At least one substrate is a protein and at least one is a - small molecule. - 'protein-reaction' - All substrates are proteins. - 'trna-reaction' - At least one substrate is a tRNA. - 'null-reaction' - No substrates or reactants are specified. - 'other' - None of the preceding cases apply. - """ - return self.sendPgdbFnCall('reaction-type', may_be_frameid(rxn)) - - def rxn_without_sequenced_enzyme_p(self, rxn, complete=None): - """ - Description - A predicate that tests if a given reaction has genes with no - associated sequence information. - Parms - rxn - An instance of the class Reactions, that is, a frame id or PFrame. - complete - Keyword, if True, the predicate will return True when there - is any associated gene without a sequence. If False, the - predicate will return True when all associated genes are - without a sequence. - - Return value - A boolean value. - """ - kwargs = {'complete': complete} - return self.sendPgdbFnCallBool('rxn-without-sequenced-enzyme-p', may_be_frameid(rxn), **kwargs) - - def pathway_hole_p(self, rxn, hole_if_any_gene_without_position=None): - """ - Description - A predicate that determines if the current reaction is - considered to be a 'pathway hole', or without an associated enzyme. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - hole_if_any_gene_without_position - Keyword, If True, then genes without specified - coordinates for the current organism's genome are not - counted when determining the status of the reaction. - - Return value - A boolean value. - """ - kwargs = {'hole-if-any-gene-without-position?': hole_if_any_gene_without_position} - return self.sendPgdbFnCallBool('pathway-hole-p', may_be_frameid(rxn), **kwargs) - - def rxn_present_p(self, rxn): - """ - Description - A predicate that determines if there is evidence for the - occurrence of the given reaction in the current PGDB. - Parms - rxn - An instance of the class Reactions, that is, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('rxn-present-p', may_be_frameid(rxn)) - - def rxn_specific_form_of_rxn_p(self, specific_rxn, generic_rxn): - """ - Description - A predicate that is True if the given generic reaction is a - generalized form of the given specific reaction. - Parms - specific_rxn - A child of the class Reactions, that is, a frame id or PFrame. - generic_rxn - A child of the class Reactions, that is, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('rxn-specific-form-of-rxn-p', may_be_frameid(specific_rxn), may_be_frameid(generic_rxn)) - - def nonspecific_forms_of_rxn(self, rxn): - """ - Description - Return all of the generic forms of the given specific reaction. - Not every reaction will necessarily have a generic form. - Parms - rxn - An instance of the class Reactions, that is, a frame id or PFrame. - - Return value - A list of children of the class Reactions. - """ - return self.sendPgdbFnCallList('nonspecific-forms-of-rxn', may_be_frameid(rxn)) - - def specific_forms_of_rxn(self, rxn): - """ - Description - Return all of the specific forms of the given generic reaction. - Not every reaction will necessarily have a specific form. - Parms - rxn - A child of the class Reactions, that is, a frame id or PFrame. - - Return value - A list of instances of the class Reactions. - """ - return self.sendPgdbFnCallList('specific-forms-of-rxn', may_be_frameid(rxn)) - - def rxn_in_compartment_p(self, rxn, compartments, default_ok=None, pwy=None, loose=None): - """ - Description - A predicate that checks if the given reaction is present in a - list of cellular compartments. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - compartments - A list of cellular compartments, as defined in the Cellular - Components Ontology. See frame CCO. - default_ok - Keyword, If True, then we return True if the - reaction has no associated compartment information, or one - of its associated locations is a super-class of one of the - members of the compartments parameter. - pwy - Keyword, a frame id or PFrame. - If supplied, the search for associated - enzymes of the parameter rxn is limited to the given child - of Pathways. - loose - Keyword, boolean. If True, then the compartments - CCO-CYTOPLASM and CCO-CYTOSOL are treated as being the - same compartment. - - Return value - A boolean value. - """ - kwargs = {'default-ok?': default_ok, 'pwy': may_be_frameid(pwy), 'loose': loose} - return self.sendPgdbFnCallBool('rxn-in-compartment-p', may_be_frameid(rxn), compartments, **kwargs) - - def compartment_of_rxn(self, rxn, default=None): - """ - Description - Returns the compartment of the reaction for non-transport - reactions. - Parms - rxn - An instance of the class Reactions, that is, a frame id or PFrame. - default - Keyword, The default compartment for reactions without any - compartment annotations on their substrates. The default - value is CCO-CYTOSOL. - - Return value - A child of the class CCO. - """ - return self.sendPgdbFnCall('compartment-of-rxn', may_be_frameid(rxn), default) - - def compartments_of_reaction(self, rxn, sides=None, default_compartment=None): - """ - Description - Returns the compartments associated with the given reaction. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - sides - Keyword, The slots of the reaction to consider. - The default value is (LEFT RIGHT). - default_compartment - Keyword, - The default compartment, as determined by the function - (default-compartment), which currently is set to - CCO-CYTOSOL. - - Return value - A list of children of the class CCO. - """ - kwargs = {'sides': sides, 'default-compartment': may_be_frameid(default_compartment)} - return self.sendPgdbFnCallList('compartments-of-reaction', may_be_frameid(rxn), **kwargs) - - def transported_chemicals(self, rxn, side=None, primary_only=None, - from_compartment=None, to_compartment=None, show_compartment=None): - """ - Description - Return the compounds in a transport reaction that change - compartments. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - side - Keyword, The side of the reaction from which to - return the transported compound. - primary_only - Keyword, If True, then filter out common - exchangers (currently defined as (PROTON NA CPD-1)+). If - True, and the only transported compounds are in this list, - then the filter doesn't apply. - from_compartment - Keyword, A compartment (child of class CCO). - If specified, then only return compounds transported from - that compartment. - to_compartment - Keyword, A compartment (child of class CCO). - If specified, then only return compounds transported to that - compartment. - show_compartment - Keyword, A compartment (child of class CCO). - If specified, and the compound is modified during transport, - then only return the form of the compound as found in this - compartment. - - Return value - A list of children of class Compounds. - """ - kwargs = {'side': side, - 'primary-only?': primary_only, - 'from-compartment': may_be_frameid(from_compartment), - 'to-compartment': may_be_frameid(to_compartment), - 'show-compartment': may_be_frameid(show_compartment)} - return self.sendPgdbFnCallList('transported-chemicals', may_be_frameid(rxn), **kwargs) - - def get_predecessors(self, rxn, pwy): - """ - Description - Return a list of all reactions that are direct predecessors - (i.e., occurr earlier in the pathway) of the given reaction in - the given pathway. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - pwy - A child of the class Pathways. - - Return value - A list of instances of the class Reactions. - """ - return self.sendPgdbFnCallList('get-predecessors', may_be_frameid(rxn), may_be_frameid(pwy)) - - def get_successors(self, rxn, pwy): - """ - Description - Return a list of all reactions that are direct successors (i.e., - occurr later in the pathway) of the given reaction in the given - pathway. - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - pwy - A child of the class Pathways. - - Return value - A list of instances of the class Reactions. - """ - return self.sendPgdbFnCallList('get-successors', may_be_frameid(rxn), may_be_frameid(pwy)) - - def rxn_w_isozymes_p(self, rxn): - """ - Description - A predicate that tests if a given reaction has any associated - isozymes (distinct proteins or protein classes that catalyze the - same reaction). - Parms - rxn - An instance of the class Reactions, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('rxn-w-isozymes-p', may_be_frameid(rxn)) - - def genes_of_pathway(self, pwy, sorted=None): - """ - Description - Return all genes coding for enzymes in the given pathway. - Parms - pwy - An instance of the class Pathways, a frame id or PFrame. - sorted? - Keyword, If True, the genes are sorted in the - order in which the corresponding reaction occurrs in the - sequence of the pathway. - - Return value - A list of instances of class Genes. - """ - kwargs = {'sorted': sorted} - return self.sendPgdbFnCallList('genes-of-pathway', may_be_frameid(pwy), **kwargs) - - def enzymes_of_pathway(self, pwy, species=None, experimental_only=None, sorted=None): - """ - Description - Return all enzymes that are present in the given pathway. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - species - Keyword, A list of species, such that in a - multi-organism PGDB such as MetaCyc, only proteins found in - those organisms will be returned. This list can include - valid org-ids, children of class Organisms, and - strings. Please see the documentation for the species - slot-unit for more information. - experimental_only - Keyword, When True, only return enzymes that have - a non-computational evidence code associated with it. - sorted - Keyword, If True, the enzymes are sorted in the - order in which the corresponding reaction occurrs in the - sequence of the pathway. - - Return value - A list of children of class Proteins or class - Protein-RNA-Complexes. - """ - kwargs = {'species': species, 'experimental-only?': experimental_only, 'sorted': sorted} - return self.sendPgdbFnCallList('enzymes-of-pathway', may_be_frameid(pwy), **kwargs) - - def compounds_of_pathway(self, pwy): - """ - Description - Return all substrates of all reactions that are within the given - pathway. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - - Return value - A list of children of class Compounds, children of class - Polymer-Segments, or strings. - """ - return self.sendPgdbFnCallList('compounds-of-pathway', may_be_frameid(pwy)) - - def substrates_of_pathway(self, pwy): - """ - Description - Bearing in mind the direction of all reactions within a pathway, - this function returns the substrates of the reactions in four - groups: a list of all reactant compounds (compounds occurring on - the left side of some reaction in the given pathway), the list - of proper reactants (the subset of reactants that are not also - products), a list of all products, and a list of all proper - products. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - - Return value - Four values as a list, each of which is a list of substrates. A substrate - may be a child of class Compounds, a child of class - Polymer-Segments, or a string. - """ - return self.sendPgdbFnCall('substrates-of-pathway', may_be_frameid(pwy)) - - def variants_of_pathway(self, pwy): - """ - Description - Returns all variants of a pathway. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - - Return value - A list of instance of the class Pathways. - """ - return self.sendPgdbFnCallList('variants-of-pathway', may_be_frameid(pwy)) - - def pathway_components(self, pwy, rxn_list=None, pred_list=None): - """ - Description - Returns all of the connected components of a pathway. A - connected component of a pathway is a set of reactions in the - pathway such that for all reactions R1 in the connected - component, a predecessor relationship holds between R1 and some - other reaction R2 in the connected component, and each connected - component is of maximal size. Every pathway will have from 1 to - N connected components, where N is the number of reactions in - the pathway. Most pathways have one connected component, but not - all. - Parms - - pwy, a frame id or PFrame. - An instance of the class Pathways, which is not a - super-pathway (i.e., does not have any entries in its - sub-pathways slot). - rxn_list - Keyword, The list of reactions to use as the starting list - of connected component clusters. Defaults to - the content of slot reaction-list in pwy. - - pred_list - Keyword, The list of reaction predecessors to iterate from - in order to cluster the reactions in rxn-list. Defaults to - list in slot predecessors of pwy. - - Return value - Returns three values as a list: the connected components as a list of - lists of the form ((r1 r2 r3) (r4 r5) (r6 r7 r8)) where each - sub-list contains all reactions in one connected component, the - number of connected components, and the length of the reaction - list. - """ - kwargs = {'rxn-list': may_be_frameid(rxn_list), 'pred-list': may_be_frameid(pred_list)} - return self.sendPgdbFnCall('pathway-components', may_be_frameid(pwy), **kwargs) - - def noncontiguous_pathway_p(self, pwy): - """ - Description - A predicate that determines if the pathway contains more than - one connected component. See function pathway-components for - more explanation. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('noncontiguous-pathway-p', may_be_frameid(pwy)) - - def rxns_adjacent_in_pwy_p(self, rxn1, rxn2, pwy): - """ - Description - A predicate to determine if two given reactions are adjacent to - one another in the given pathway. - Parms - - rxn1 - An instance of the class Reactions, a frame id or PFrame. - rxn2 - An instance of the class Reactions, a frame id or PFrame. - pwy - An instance of the class Pathways, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('rxns-adjacent-in-pwy-p', may_be_frameid(rxn1), may_be_frameid(rxn2), may_be_frameid(pwy)) - - def cofactors_and_pgroups_of_enzrxn(self, enzrxn): - """ - Description - Returns the cofactors and prosthetic groups of an enzymatic - reaction. - Parms - - enzrxn - An instance of the class Enzymatic-Reactions, a frame id or PFrame. - - Return value - A list of children of class Chemicals or strings, - representing cofactors and/or prosthetic groups. - """ - return self.sendPgdbFnCallList('cofactors-and-pgroups-of-enzrxn', may_be_frameid(enzrxn)) - - def enzrxn_activators(self, er, phys_relevant_only=None): - """ - Description - Returns the list of activators (generally small molecules) of - the enzymatic reaction frame. - Parms - - er - An instance of the class Enzymatic-Reactions, a frame id or PFrame. - phys_relevant_only - Keyword, If True, then only return activators that are - associated with Regulation instances that have the - physiologically-relevant? slot set to True. - - Return value - A list of children of the class Chemicals. - """ - # phys_relevant_only is optional for the Lisp version - return self.sendPgdbFnCallList('enzrxn-activators', may_be_frameid(er), phys_relevant_only) - - def enzrxn_inhibitors(self, er, phys_relevant_only=None): - """ - Description - Returns the list of inhibitors (generally small molecules) of - the enzymatic reaction frame. - Parms - - er - An instance of the class Enzymatic-Reactions, a frame id or PFrame. - phys_relevant_only - Keyword, If True, then only return inhibitors that are - associated with Regulation instances that have the - physiologically-relevant? slot set to True. - - Return value - A list of children of the class Chemicals. - """ - # phys_relevant_only is optional for the Lisp version - return self.sendPgdbFnCallList('enzrxn-inhibitors', may_be_frameid(er), phys_relevant_only) - - def pathways_of_enzrxn(self, enzrxn, include_super_pwys=None): - """ - Description - Returns the list of pathways in which the given enzymatic - reaction participates. - Parms - - enzrxn - An instance of the class Enzymatic-Reactions, a frame id or PFrame. - include_super_pwys - Keyword, If True, then not only will the - direct pathways in which enzrxn is associated in be - returned, but also any enclosing super-pathways. If enzrxn - is associated with a reaction that is directly associated - with a super-pathway, then the function might return - super-pathways even if this option is nil. - - Return value - A list of instances of class Pathways. - """ - kwargs = {'include-super-pwys?': include_super_pwys} - return self.sendPgdbFnCallList('pathways-of-enzrxn', may_be_frameid(enzrxn), **kwargs) - - def pathway_allows_enzrxn(self, pwy, rxn, enzrxn, single_species=None): - """ - Description - A predicate which returns a True value if the given pathway - allows the given enzymatic reaction to catalyze the given - reaction. Certain pathways have a list of enzymatic reactions - that are known not to catalyze certain reactions. See the - documentation of slot-unit enzyme-use for more information. - Parms - - pwy - An instance of the class Pathways, a frame id or PFrame. - rxn - An instance of the class Reactions, a frame id or PFrame. - enzrxn - An instance of the class Enzymatic-Reactions, a frame id or PFrame. - single_species - Keyword, An instance of the class Organisms If set, - then enzrxn has the further stricture that it must be an - enzymatic reaction present in the organism specified by the - value passed to single-species. - - Return value - A boolean value. - """ - # single_species is optional for the Lisp version. - return self.sendPgdbFnCallBool('pathway-allows-enzrxn', may_be_frameid(pwy), may_be_frameid(rxn), may_be_frameid(enzrxn), single_species) - - def monomers_of_protein(self, p, coefficients=None, unmodify=None): - """ - Description - Returns the monomers of the given protein complex. - Parms - - p - An instance of the class Proteins, a frame id or PFrame. - coefficients - Keyword, If True, then the second return value of - the function will be a list of monomer coefficients. - Defaults to True. - unmodify - Keyword, If True, obtain the monomers of the - unmodified form of p. - - Return value - First value is a list of instances of the class Proteins. If - coefficients? is True, then the second value is the - corresponding coefficients of the monomers fromthe first return - value. - """ - kwargs = {'coefficients?': coefficients, 'unmodify?': unmodify} - return self.sendPgdbFnCallList('monomers-of-protein', may_be_frameid(p), **kwargs) - - def base_components_of_protein(self, p, exclude_small_molecules=None): - """ - Description - Same as function monomers-of-protein, but also returns - components of the protein that are RNAs or compounds, not just - polypeptides. - Parms - - p - An instance of the class Proteins, a frame id or PFrame. - exclude_small_molecules - Keyword, If nil, then small molecule components - are also returned. Default value is True. - - Return value - Two values as a list. The first value is a list of the components, which - can be instances of the following classes: Polypeptides, - RNA, and Compounds. The second value is a list of the - corresponding coefficients of the components in the first value. - """ - kwargs = {'exclude-small-molecules?': exclude_small_molecules} - return self.sendPgdbFnCall('base-components-of-protein', may_be_frameid(p), **kwargs) - - def containers_of(self, protein, exclude_self=None): - """ - Description - Return all complexes of which the given protein is a direct or - indirect component. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - exclude_self - Keyword, If True, then protein will not be included in - the return value. - - Return value - A list of instances of the class Proteins. - """ - # exclude_self is an optional parameter for the Lisp fn version. - return self.sendPgdbFnCallList('containers-of', may_be_frameid(protein), exclude_self) - - def protein_or_rna_containers_of(self, protein, exclude_self=None): - """ - Description - This function is the same as the function containers-of, - except that it only includes containers that are instances of - either class Protein-Complexes, or class - Protein-RNA-Complexes. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - exclude_self - Keyword, If True, then protein will not be included in - the return value. - - Return value - A list of instances of the class Proteins. - """ - # exclude_self is an optional parameter for the Lisp fn version. - return self.sendPgdbFnCallList('protein-or-rna-containers-of', may_be_frameid(protein), exclude_self) - - def homomultimeric_containers_of(self, protein, exclude_self=None): - """ - Description - This function is the same as the function containers-of, - except that it only includes containers that are homomultimers. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - exclude_self - Keyword, If True, then protein will not be included in - the return value. - - Return value - A list of instances of the class Proteins. - """ - # exclude_self is an optional parameter for the Lisp fn version. - return self.sendPgdbFnCallList('homomultimeric-containers-of', may_be_frameid(protein), exclude_self) - - def polypeptide_or_homomultimer_p(self, protein): - """ - Description - A predicate that determines if the given protein is a - polypeptide or a homomultimer. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('polypeptide-or-homomultimer-p', may_be_frameid(protein)) - - def unmodified_form(self, protein): - """ - Description - Return the unmodified form of the given protein, which might be - the same as the given protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - An instance of the class Proteins. - """ - return self.sendPgdbFnCall('unmodified-form', may_be_frameid(protein)) - - def unmodified_or_unbound_form(self, protein): - """ - Description - Return the unmodified form or unbound (to a small molecule) form - of the given protein, which might be the same as the given protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - An instance of the class Proteins. - """ - return self.sendPgdbFnCall('unmodified-or-unbound-form', may_be_frameid(protein)) - - def reduce_modified_proteins(self, prots, debind=None): - """ - Description - Given a list of proteins, the function converts all of the - proteins to their unmodified form, and then removes any - duplicates from the subsequent list. - Parms - - prots - A list of instances of the class Proteins, a frame id or PFrame. - debind - Keyword, When True, the proteins are further - simplified by obtaining the unbound form of the protein, if - it is bound to a small molecule. - - Return Value - A list of instances of the class Proteins. - """ - kwargs = {'debind?': debind} - return self.sendPgdbFnCallList('reduce-modified-proteins', may_be_frameid(prots), **kwargs) - - def all_direct_forms_of_protein(self, protein): - """ - Description - Given a protein, this function will return all of the directly - related proteins of its modified and unmodified forms, meaning - all of their direct subunits and all of their direct containers. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return Value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('all-direct-forms-of-protein', may_be_frameid(protein)) - - def all_forms_of_protein(self, protein): - """ - Description - Given a protein, this function will return all of the related - proteins of its modified and unmodified forms, meaning all of - their subunits and all of their containers. Unlike - all_direct_forms_of_protein, this function is not limited to - the direct containers only. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('all-forms-of-protein', may_be_frameid(protein)) - - def modified_forms(self, protein, exclude_self=None, all_variants=None): - """ - Description - Returns all modified forms of a protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - exclude_self - Keyword, If True, then protein will not be included in - the return value. - all_variants - Keyword, If True, and protein is a modified form, then - we return all of the modified forms of the unmodified forms - of protein. - - Return value - A list of instances of the class Proteins. - """ - # Parameters exclude_self and all_variants are optionals for the Lisp fn version. - return self.sendPgdbFnCallList('modified-forms', may_be_frameid(protein), exclude_self, all_variants) - - def modified_and_unmodified_forms(self, protein): - """ - Description - Returns all of the modified and unmodified forms of the given - protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('modified-and-unmodified-forms', may_be_frameid(protein)) - - def modified_containers(self, protein): - """ - Description - Returns all containers of a protein (including itself), and all - modified forms of the containers. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('modified-containers', may_be_frameid(protein)) - - def top_containers(self, protein): - """ - Description - Return the top-most containers (i.e., they are not a component - of any other protein complex) of the given protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('top-containers', may_be_frameid(protein)) - - def small_molecule_cplxes_of_prot(self, protein): - """ - Description - Return all of the forms of the given protein that are complexes - with small molecules. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('small-molecule-cplxes-of-prot', may_be_frameid(protein)) - - def genes_of_protein(self, protein): - """ - Description - Given a protein, return the set of genes which encode all of the - monomers of the protein. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Genes. - """ - return self.sendPgdbFnCallList('genes-of-protein', may_be_frameid(protein)) - - def genes_of_proteins(self, protein): - """ - Description - The same as genes_of_protein, except that it takes a list of - proteins and returns a set of genes. - Parms - - protein - A list of instances of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Genes. - """ - return self.sendPgdbFnCallList('genes-of-proteins', may_be_frameid(protein)) - - def reactions_of_enzyme(self, protein, kb=None, include_specific_forms=None): - """ - Description - Return all of the reactions associated with a given protein via - enzymatic reactions. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - kb - Keyword, The KB object of the KB in which to find - the associated reactions. Defaults to self. - include_specific_forms - Keyword, When True, specific forms of associated - generic reactions are also returned. Default value is True. - - Return value - A list of instances of the class Reactions. - """ - kwargs = {'kb': kb, 'include-specific-forms?': include_specific_forms} - return self.sendPgdbFnCallList('reactions-of-enzyme', may_be_frameid(protein), **kwargs) - - def species_of_protein(self, protein): - """ - Description - Get the associated species for the given protein. - Parms - - protein - A list of instances of the class Proteins, a frame id or PFrame. - - Return value - An instance of the class Organisms, or a string. - """ - return self.sendPgdbFnCall('species-of-protein', may_be_frameid(protein)) - - def enzyme_p(self, protein, type=None): - """ - Description - Predicate that determines whether a specified protein is an - enzyme or not. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - type - Keyword, Can take on one of the following values to select - more precisely what is meant by an "enzyme": - - 'any' - Any protein that catalyzes a reaction is considered an - enzyme. - 'chemical-change' - If the reactants and products of the catalyzed reactin - differ, and not just by their cellular location, then - the protein is considered an enzyme. - 'small-molecule' - If the reactants of the catalyzed reaction differ and - are small molecules, then the protein is considered an - enzyme. - 'transport' - If the protein catalyzes a transport reaction. - 'non-transport' - If the protein only catalyzes non-transport reactions. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('enzyme-p', may_be_frameid(protein), mkey(type)) - - def leader_peptide_p(self, protein): - """ - Description - A predicate that determines whether the given protein is a - leader peptide. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('leader-peptide-p', may_be_frameid(protein)) - - def protein_p(self, frame): - """ - Description - A predicate that determines whether the given frame is a protein. - Parms - - frame - a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('protein-p', may_be_frameid(frame)) - - def complex_p(self, frame): - """ - Description - A predicate that determines whether the given frame is a - protein complex. - Parms - - frame - a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('complex-p', may_be_frameid(frame)) - - def reactions_of_protein(self, protein, check_protein_components=None, - check_protein_containers=None): - """ - Description - Returns all of the associated reactions that the given protein, - or its components, catalyzes. - Parms - - protein - An instance of the class Proteins, a frame id or PFrame. - check_protein_components? - Keyword, If True, check all components of this protein for - catalyzed reactions. Defaults to True. - check_protein_containers? - Keyword, If True, check the containers and modified forms - of the protein for catalyzed reactions. - - Return value - A list of instances of class Reactions. - """ - return self.sendPgdbFnCallList('reactions-of-protein', may_be_frameid(protein), - check_protein_components, check_protein_containers) - - def protein_in_compartment_p(self, rxn, compartments, default_ok=None, pwy=None, loose=None): - """ - Description - A predicate that checks if the given reaction is present in a - list of cellular compartments. - Parms - - rxn - An instance of the class Reactions, a frame id or PFrame. - compartments - A list of cellular compartments, as defined in the Cellular - Components Ontology. See frame CCO. - default_ok - Keyword, If True, then we return True if the - reaction has no associated compartment information, or one - of its associated locations is a super-class of one of the - members of the compartments parameter. - pwy - Keyword, a frame id or PFrame. If supplied, the search for associated - enzymes of the parameter rxn is limited to the given child - of Pathways. - loose - Keyword, If True, then the compartments - CCO-CYTOPLASM and CCO-CYTOSOL are treated as being the - same compartment. - - Return value - A boolean value. - """ - kwargs = {'default-ok?': default_ok, 'pwy': may_be_frameid(pwy), 'loose?': loose} - return self.sendPgdbFnCallBool('protein-in-compartment-p', may_be_frameid(rxn), **kwargs) - - def all_transporters_across(self, membranes=None, method=None): - """ - Description - Returns a list of transport proteins that transport across one - of the given membranes. - Parms - membranes - Keyword, Either all or a list of instances of the class. - Defaults to all CCO-MEMBRANE. - method - Keyword, - Either 'location' or 'reaction-compartments'. 'location' - will check the locations slot, while - 'reaction-compartments' will examine the compartments of - reaction substrates. Default value is 'location'. - - Return value - A list of instances of class Proteins. - """ - kwargs = {'membranes': may_be_frameid(membranes), 'method': method} - return self.sendPgdbFnCallList('all-transporters-across', **kwargs) - - def autocatalytic_reactions_of_enzyme(self, protein): - """ - Description - Returns a list of reaction frames, where the protein - participates as a substrate of the reaction, and the reaction - has no associated Enzymatic Reaction frame. This implies that - the protein substrate of the reaction might autocatalyzing the - reaction. - Parms - protein - An instance frame of class Proteins, a frame id or PFrame. - - Return value - A list of instances of class Reactions. - """ - return self.sendPgdbFnCallList('autocatalytic-reactions-of-enzyme', may_be_frameid(protein)) - - def gene_p(self, item): - """ - Description - A predicate to determine if the given frame is a gene. - Parms - item - a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('gene-p', may_be_frameid(item)) - - def enzymes_of_gene(self, gene): - """ - Description - Collects all of the enzymes encoded by the given gene, including - modified forms and complexes in which it is a sub-component. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('enzymes-of-gene', may_be_frameid(gene)) - - def all_products_of_gene(self, gene): - """ - Description - Collects all proteins (not necessarily enzymes) that are encoded - by the given gene. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('all-products-of-gene', may_be_frameid(gene)) - - def reactions_of_gene(self, gene): - """ - Description - Returns all reactions catalyzed by enzymes encoded by the given - gene. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - A list of instances of class Reactions. - """ - return self.sendPgdbFnCallList('reactions-of-gene', may_be_frameid(gene)) - - def pathways_of_gene(self, gene, include_super_pwys=None): - """ - Description - Returns the pathways of enzymes encoded by the given gene. - Parms - gene - An instance of class Genes, a frame id or PFrame. - include_super_pwys - Keyword, If True, then not only will the - direct pathways in which gene encodes an enzyme be - returned, but also any enclosing super-pathways. If gene - is associated with a reaction that is directly associated - with a super-pathway, then the function might return - super-pathways even if this option is nil. - - Return value - A list of instances of class Pathways. - """ - kwargs = {'include-super-pwys': include_super_pwys} - return self.sendPgdbFnCallList('pathways-of-gene', may_be_frameid(gene), **kwargs) - - def chromosome_of_gene(self, gene): - """ - Description - Returns the replicon on which the gene is located. If the gene - is located on a contig that is, in turn, part of a chromosome, - then the contig is returned. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - An instance of class Genetic-Elements. - """ - return self.sendPgdbFnCall('chromosome-of-gene', may_be_frameid(gene)) - - def unmodified_gene_product(self, gene): - """ - Description - Returns the first element of the list returned by the function - unmodified-gene-products. This is useful if you are sure that - there are no alternative splice forms of your gene. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - An instance of either class Polypeptides or 'RNA. - """ - return self.sendPgdbFnCall('unmodified-gene-product', may_be_frameid(gene)) - - def unmodified_gene_products(self, gene): - """ - Description - Return all of the unmodified gene products (i.e. alternative - splice forms) of the given gene. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - A list of instances of either class Polypeptides or 'RNA. - """ - return self.sendPgdbFnCallList('unmodified-gene-products', may_be_frameid(gene)) - - def next_gene_on_replicon(self, gene): - """ - Description - Return the next gene on the replicon. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - Returns two values as a list. The first value is the next gene, or nil if - there is not a next gene (i.e., the gene is at the end of a - linear replicon). The second value is 'last' if the gene is the - last gene on a linear replicon. - """ - return self.sendPgdbFnCall('next-gene-on-replicon', may_be_frameid(gene)) - - def previous_gene_on_replicon(self, gene): - """ - Description - Return the previous gene on the replicon. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - Returns two values as a list. The first value is the previous gene, or nil - if there is not a previous gene (i.e., the gene is at the - beginning of a linear replicon). The second value is 'first' if - the gene is the first gene on a linear replicon. - """ - return self.sendPgdbFnCall('previous-gene-on-replicon', may_be_frameid(gene)) - - def adjacent_genes_p(self, g1, g2): - """ - Description - Given two genes, this predicate will return True if they are on - the same replicon, and adjacent to one another. - Parms - g1 - An instance of class Genes, a frame id or PFrame. - g2 - An instance of class Genes, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('adjacent-genes?', may_be_frameid(g1), may_be_frameid(g2)) - - def neighboring_genes_p(self, g1, g2, n=None): - """ - Description - Given two genes, this predicate determines if the two genes are - "neighbors", or within a certain number of genes from one - another along the replicon. - Parms - g1 - An instance of class Genes, a frame id or PFrame. - g2 - An instance of class Genes, a frame id or PFrame. - n - Keyword, An integer representing the number of genes g1 - and g2 can be from one another. Default value is 10. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('neighboring-genes-p', may_be_frameid(g1), may_be_frameid(g2), n) - - def gene_clusters(self, genes, max_gap=None): - """ - Description - Groups together genes based on whether each gene is a gene - neighbor with other genes. - Parms - genes - A list of instances of class Genes, a frame id or PFrame. - max_gap - Keyword, An integer representing the number of genes any - pair from genes can be from one another. Default value is 10. - - Return value - A list of lists, where the first element of each sub-list is a - gene from genes, and the rest of the list are all of the gene - neighbors of the first gene. - """ - return self.sendPgdbFnCallList('gene-clusters', may_be_frameid(genes), max_gap) - - def rna_coding_gene(self, gene): - """ - Description - A predicate that determines if the given gene encodes an RNA. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('rna-coding-gene', may_be_frameid(gene)) - - def protein_coding_gene(self, gene): - """ - Description - A predicate that determines if the given gene encodes a protein - (as opposed to an RNA). - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('protein-coding-gene', may_be_frameid(gene)) - - def pseudo_gene_p(self, gene): - """ - Description - A predicate that determines if the given gene is a pseudo-gene. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('pseudo-gene-p', may_be_frameid(gene)) - - def phantom_gene_p(self, gene): - """ - Description - A predicate that determines if the given gene is a phantom gene. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('phantom-gene-p', may_be_frameid(gene)) - - def dna_binding_site_p(self, gene): - """ - Description - A predicate that determines if the given frame is an instance of - the class DNA-Binding-Sites. - Parms - gene - A frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('dna-binding-site-p', may_be_frameid(gene)) - - def terminator_p(self, gene): - """ - Description - A predicate that determines if the given object is an instance - of the class Terminators. - Parms - gene - A frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('terminatorp', may_be_frameid(gene)) - - def operon_of_gene(self, gene): - """ - Description - Given a gene, return a list of transcription units that form the - operon containing the gene. - Parms - gene - An instance of class Genes, a frame id or PFrame - - Return value - A list of instances of class Transcription-Units. - """ - return self.sendPgdbFnCallList('operon-of-gene', may_be_frameid(gene)) - - def genes_in_same_operon(self, gene): - """ - Description - Given a gene, return all other genes in the same operon. - Parms - gene - An instance of class Genes, a frame id or PFrame. - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('genes-in-same-operon', may_be_frameid(gene)) - - def gene_transcription_units(self, gene): - """ - Description - Given a gene, return all of the transcription units which - contain the gene. - Parms - gene - An instance of class Genes, a frame id or PFrame - - Return value - A list of instances of class Transcription-Units. - """ - return self.sendPgdbFnCallList('gene-transcription-units', may_be_frameid(gene)) - - def cotranscribed_genes(self, gene): - """ - Description - Return all co-transcribed genes (i.e., genes which are a part of - one or more of the same transcription units) of the given gene. - Parms - gene - An instance of class Genes, a frame id or PFrame - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('cotranscribed-genes', may_be_frameid(gene)) - - def terminators_affecting_gene(self, gene): - """ - Description - Find terminators in the same transcription unit and upstream of - the given gene. - Parms - gene - An instance of class Genes, a frame id or PFrame - - Return value - A list of instances of class Terminators. - """ - return self.sendPgdbFnCallList('terminators-affecting-gene', may_be_frameid(gene)) - - def chromosome_of_object(self, item): - """ - Description - Given a frame object, the replicon where it is located is returned. - If there is no associated replicon for the object, nil is - returned. If the object is on more than one replicon, an error - is thrown. - Parms - item, a frame id or PFrame - An instance of class All-Genes, Transcription-Units, - Promoters, Terminators, Misc-Features, or - DNA-Binding-Sites. - - Return value - An instance of class Genetic-Elements. - """ - return self.sendPgdbFnCall('chromosome-of-object', may_be_frameid(item)) - - def activation_p(self, reg_frame): - """ - Description - A predicate that determines if a given regulation frame is - describing activation. - Parms - reg_frame - An instance of class Regulation, a frame id or PFrame - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('activation-p', may_be_frameid(reg_frame)) - - def inhibition_p(self, reg_frame): - """ - Description - A predicate that determines if a given regulation frame is - describing inhibition. - Parms - reg_frame - An instance of class Regulation, a frame id or PFrame - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('inhibition-p', may_be_frameid(reg_frame)) - - def direct_regulators(self, item, filter_fn=None): - """ - Description - Return all regulators that are connected to a regulated object - by a single regulation object. - Parms - item - A frame id or PFrame. - filter_fn - Keyword, A predicate used to filter the regulation objects - used to find the regulators. - - Return value - A list of frames that regulate item. - """ - kwargs = {'filter-fn': filter_fn} - return self.sendPgdbFnCallList('direct-regulators', may_be_frameid(item), **kwargs) - - def direct_activators(self, item): - """ - Description - Return all activators that are connected to an activated object - by a single regulation object. - Parms - item - A frame id or PFrame. - - Return value - A list of frames that activate item. - """ - return self.sendPgdbFnCallList('direct-activators', may_be_frameid(item)) - - def direct_inhibitors(self, item): - """ - Description - Return all inhibitors that are connected to an inhibited object - by a single regulation object. - Parms - item - A frame id or PFrame. - - Return value - A list of frames that inhibit item. - """ - return self.sendPgdbFnCallList('direct-inhibitors', may_be_frameid(item)) - - def transcription_factor_p(self, protein, include_inactive=None): - """ - Description - A predicate that determines if the given protein is a - transcription factor, or a component of a transcription factor. - Parms - protein - An instance frame of class Proteins, a frame id or PFrame. - include_inactive - Keyword, If True, then the function checks to see - if any of its components or containers is a transcription - factor as well. - - Return value - A boolean value. - """ - kwargs = {'include-inactive?': include_inactive} - return self.sendPgdbFnCallBool('transcription-factor-p', may_be_frameid(protein), **kwargs) - - def regulator_of_type(self, protein, class_name): - """ - Description - A predicate that determines if the given protein is a regulator - of the specified class. - Parms - protein - An instance frame of class Proteins, a frame id or PFrame. - class - A subclass of Regulation. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('regulator-of-type', may_be_frameid(protein), class_name) - - def regulon_of_protein(self, protein): - """ - Description - Returns all transcription units regulated by any form of the - given protein. - Parms - protein - An instance frame of class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Transcription-Units. - """ - return self.sendPgdbFnCallList('regulon-of-protein', may_be_frameid(protein)) - - def regulation_frame_transcription_units(self, reg_frame): - """ - Description - Given a regulation object, return the transcription units when - one of the regulated entities is a promoter or terminator of the - transcription unit. - Parms - reg_frame - An instance of the class Regulation-of-Transcription, a frame id or PFrame. - - Return value - A list of instances of the class Transcription-Units. - """ - return self.sendPgdbFnCallList('regulation-frame-transcription-units', may_be_frameid(reg_frame)) - - def transcription_unit_regulation_frames(self, tu): - """ - Description - Returns a list of regulation frames that regulate the - transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of the class Regulation. - """ - return self.sendPgdbFnCallList('transcription-unit-regulation-frames', may_be_frameid(tu)) - - def transcription_unit_activation_frames(self, tu): - """ - Description - Returns a list of regulation frames that activate the - transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of the class Regulation. - """ - return self.sendPgdbFnCallList('transcription-unit-activation-frames', may_be_frameid(tu)) - - def transcription_unit_inhibition_frames(self, tu): - """ - Description - Returns a list of regulation frames that inhibit the - transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of the class Regulation. - """ - return self.sendPgdbFnCallList('transcription-unit-inhibition-frames', may_be_frameid(tu)) - - def transcription_units_of_protein(self, protein): - """ - Description - Return all of the transcription units for which the given - protein, or its modified form, acts as a regulator. - Parms - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Transcription-Units. - """ - return self.sendPgdbFnCallList('transcription-units-of-protein', may_be_frameid(protein)) - - def genes_regulated_by_protein(self, protein): - """ - Description - Return all of the genes for which the given protein, or its - modified form, acts as a regulator. - Parms - protein - An instance of the class Proteins, a frame id or PFrame. - - Return value - A list of instances of the class Genes. - """ - return self.sendPgdbFnCallList('genes-regulated-by-protein', may_be_frameid(protein)) - - def DNA_binding_sites_of_protein(self, tf, all_forms=None): - """ - Description - Given a transcription factor, return all of its DNA binding sites. - Parms - tf - An instance of the class Proteins, a frame id or PFrame. - all_forms - Keyword, When True, then return the DNA binding - sites of modified forms and subunits of tf as well. - - Return value - A list of instances of the class DNA-Binding-Sites. - """ - kwargs = {'all-forms?': all_forms} - return self.sendPgdbFnCallList('DNA-binding-sites-of-protein', may_be_frameid(tf), **kwargs) - - def regulator_proteins_of_transcription_unit(self, tu): - """ - Description - Returns all transcription factors that regulate the given - transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('regulator-proteins-of-transcription-unit', may_be_frameid(tu)) - - def transcription_factor_ligands(self, tfs, mode): - """ - Description - For a single transcription factor or list of transcription - factors, return all transcription factor ligands. - Parms - tfs, a frame id or PFrame or a list of these. - An instance or a list of instances of the class - Proteins. If tfs is not the active form, then the - active form is determined automatically. - mode - One of the following values: 'activator', 'inhibitor', or - 'both'. - - Return value - A list of instances of the class Chemicals or strings. - """ - return self.sendPgdbFnCallList('transcription-factor-ligands', may_be_frameid(tfs), mkey(mode)) - - def transcription_factor_active_forms(self, tfs): - """ - Description - For a given transcription factor, find all active forms (i.e, - form of the protein that regulates) of the transcription factor. - Parms - tfs, a frame id or PFrame. - An instance of the class Proteins. - - Return value - A list of instances of the class Proteins. - """ - return self.sendPgdbFnCallList('transcription-factor-active-forms', may_be_frameid(tfs)) - - def genes_regulating_gene(self, gene): - """ - Description - Return all genes regulating the given gene by means of a - transcription factor. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('genes-regulating-gene', may_be_frameid(gene)) - - def genes_regulated_by_gene(self, gene): - """ - Description - Return all genes regulated by the given gene by means of a - transcription factor. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('genes-regulated-by-gene', may_be_frameid(gene)) - - def regulators_of_gene_transcription(self, gene, by_function=None): - """ - Description - Returns a list of proteins that are regulators of the given gene. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - by_function - Keyword, If True, then return two values: a list of - activator proteins and a list of inhibitor proteins. - - Return value - A list of instances of class Proteins. If by_function is - True, then two values are returned. The first value is a list - of activator proteins, and the second value is a list of - inhibitor proteins. - """ - kwargs = {'by-function?' : by_function} - return self.sendPgdbFnCall('regulators-of-gene', may_be_frameid(gene), **kwargs) - - def transcription_unit_activators(self, tu): - """ - Description - Returns all activator proteins of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('transcription-unit-activators', may_be_frameid(tu)) - - def transcription_unit_inhibitors(self, tu): - """ - Description - Returns all inhibitor proteins of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('transcription-unit-inhibitors', may_be_frameid(tu)) - - def regulators_of_operon_transcription(self, operon_list, by_function=None): - """ - Description - Returns a list of transcription factors of an operon. - Parms - operon_list - A list of instances of the class Transcription-Units, a frame id or PFrame. - by_function - Keyword, If True, then return two values: a list of - activator proteins and a list of inhibitor proteins. - - Return value - A list of instances of class Proteins. If the modified form - of the protein is the transcription factor, then that is the - protein returned. - """ - # Parameter by_function is optional for the Lisp fn. - return self.sendPgdbFnCallList('regulators-of-operon-transcription', may_be_frameid(operon_list), by_function) - - def transcription_unit_promoter(self, tu): - """ - Description - Returns the promoter of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - An instance of class Promoters. - """ - return self.sendPgdbFnCall('transcription-unit-promoter', may_be_frameid(tu)) - - def transcription_unit_genes(self, tu): - """ - Description - Returns the genes of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class Genes. - """ - return self.sendPgdbFnCallList('transcription-unit-genes', may_be_frameid(tu)) - - def transcription_unit_first_gene(self, tu): - """ - Description - Returns the first gene of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - An instance of class Genes. - """ - return self.sendPgdbFnCall('transcription-unit-first-gene', may_be_frameid(tu)) - - def transcription_unit_binding_sites(self, tu): - """ - Description - Returns the binding sites of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class DNA-Binding-Sites. - """ - return self.sendPgdbFnCallList('transcription-unit-binding-sites', may_be_frameid(tu)) - - def transcription_unit_transcription_factors(self, tu): - """ - Description - Returns the binding sites of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class DNA-Binding-Sites. - """ - return self.sendPgdbFnCallList('transcription-unit-transcription-factors', may_be_frameid(tu)) - - def transcription_unit_mrna_binding_sites(self, tu): - """ - Description - Returns the mRNA binding sites of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class mRNA-Binding-Sites. - """ - return self.sendPgdbFnCallList('transcription-unit-mrna-binding-sites', may_be_frameid(tu)) - - def chromosome_of_operon(self, tu): - """ - Description - Returns the replicon of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - An instance of class Genetic-Elements. - """ - return self.sendPgdbFnCall('chromosome-of-operon', may_be_frameid(tu)) - - def binding_sites_affecting_gene(self, gene): - """ - Description - Returns all binding sites which are present in the same - transcription units as the given gene. - Parms - gene - An instance of the class Genes, a frame id or PFrame. - - Return value - A list of instances of class DNA-Binding-Sites. - """ - return self.sendPgdbFnCallList('binding-sites-affecting-gene', may_be_frameid(gene)) - - def binding_site_to_regulators(self, bsite): - """ - Description - Returns all of the transcription factors of the given binding site. - Parms - bsite - An instance of class DNA-Binding-Sites, a frame id or PFrame. - - Return value - A list of instances of class Proteins. - """ - return self.sendPgdbFnCallList('binding-site->regulators', may_be_frameid(bsite)) - - def transcription_units_of_promoter(self, promoter): - """ - Description - Returns all transcription units of a given promoter. - Parms - promoter - An instance of class Promoters, a frame id or PFrame. - - Return value - A list of instances of class Transcription-Units. - """ - return self.sendPgdbFnCallList('transcription-units-of-promoter', may_be_frameid(promoter)) - - def promoter_binding_sites(self, promoter): - """ - Description - Returns all of the binding sites associated with the given - promoter, across multiple transcription units. - Parms - promoter - An instance of class Promoters, a frame id or PFrame. - - Return value - A list of instances of class DNA-Binding-Sites. - """ - return self.sendPgdbFnCallList('promoter-binding-sites', may_be_frameid(promoter)) - - def transcription_unit_terminators(self, operon): - """ - Description - Returns the terminators of the given transcription unit. - Parms - operon - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class Terminators. - """ - return self.sendPgdbFnCallList('transcription-unit-terminators', may_be_frameid(operon)) - - def containing_tus(self, site): - """ - Description - Given a site (whether a DNA binding site, a promoter, a gene, or - a terminator) along a transcription unit, return the - correspodning transcription units. - Parms - site, a frame id or PFrame. - An instance of class Transcription-Units, - mRNA-Binding-Sites, DNA-Binding-Sites, - Promoters, Genes, or Terminators. - - Return value - A list of instances of class Transcription-Units. - """ - return self.sendPgdbFnCallList('containing-tus', may_be_frameid(site)) - - def containing_chromosome(self, site): - """ - Description - Given a site (whether a DNA binding site, a promoter, a gene, or - a terminator) along a transcription unit, return the - correspodning regulon. - Parms - site, a frame id or PFrame. - An instance of class Transcription-Units, - mRNA-Binding-Sites, DNA-Binding-Sites, - Promoters, Genes, or Terminators. - - Return value - An instance of class Genetic-Elements. - """ - return self.sendPgdbFnCall('containing-chromosome', may_be_frameid(site)) - - def binding_site_promoters(self, tu): - """ - Description - Returns the promoters of the given DNA binding site. - Parms - tu - An instance of the class DNA-Binding-Sites, a frame id or PFrame. - - Return value - A list of instances of class Promoters. - """ - return self.sendPgdbFnCallList('binding-site-promoters', may_be_frameid(tu)) - - def transcription_unit_all_components(self, tu): - """ - Description - Returns all components (binding sites, promoters, genes, - terminators) of the given transcription unit. - Parms - tu - An instance of the class Transcription-Units, a frame id or PFrame. - - Return value - A list of instances of class Transcription-Units, - mRNA-Binding-Sites, DNA-Binding-Sites, Promoters, - Genes, or Terminators. - """ - return self.sendPgdbFnCallList('transcription-unit-all-components', may_be_frameid(tu)) - - def binding_site_transcription_units(self, promoter): - """ - Description - Returns all transcription units of a given binding site. - Parms - promoter, a frame id or PFrame. - An instance of class DNA-Binding-Sites or - mRNA-Binding-Sites. - - Return value - A list of instances of class Transcription-Units. - """ - return self.sendPgdbFnCallList('binding-site-transcription-units', may_be_frameid(promoter)) - - def reactions_of_compound(self, cpd, non_specific_too=None,transport_only=None,compartment=None,enzymatic=None): - """ - Description - Return all reactions in which the given compound participates as - a substrate. - Parms - cpd, a frame id or PFrame. - A child of class Compounds. - non_specific_too - Keyword, If True, returns all generic - reactions where cpd, or a parent of cpd, appears as a - substrate. - transport_only - Keyword, If True, return only transport reactions. - compartment - Keyword, If True, return only reactions within - the specified compartment. - enzymatic - Keyword, If True, return only enzymatic reactions. - - Return value - A list of children of class Reactions. - """ - kwargs = {'non-specific-too?': non_specific_too, - 'transport-only?': transport_only, - 'compartment': compartment, - 'enzymatic?': enzymatic } - return self.sendPgdbFnCallList('reactions-of-compound', may_be_frameid(cpd), **kwargs) - - def substrate_of_generic_rxn(self, cpd, rxn): - """ - Description - A predicate that determines if a parent of the given compound is - a substrate of the given generic reaction. - Parms - cpd - An instance of class Compounds, a frame id or PFrame. - rxn - An instance of class Reactions, a frame id or PFrame. - - Return value - A boolean value. - """ - return self.sendPgdbFnCallBool('substrate-of-generic-rxn', may_be_frameid(cpd), may_be_frameid(rxn)) - - def pathways_of_compound(self, cpd, non_specific_too=None, modulators=None, phys_relevant=None, include_rxns=None): - """ - Description - Returns all pathways in which the given compound appears as a - substrate. - Parms - cpd - An instance of class Compounds, a frame id or PFrame. - non-specific_too - Keyword, If True, returns all generic - reactions where cpd, or a parent of cpd, appears as a - substrate. - modulators - Keyword, If True, returns pathways where cpd - appears as a regulator as well. - phys-relevant - Keyword, If True, then only return inhibitors - that are associated with Regulation instances that have - the physiologically-relevant? slot set to True. - include-rxns - Keyword, If True, then return a list of - reaction-pathway pairs. - - Return value - A list of instances of class Pathways. If include-rxns? is - True, then a list of lists, where each sub-list consists of - an instance of class Reactions and an instance of class - Pathways. - """ - kwargs = {'non-specific-too?': non_specific_too, - 'modulators?': modulators, - 'phys-relevant?': phys_relevant, - 'include-rxns?': include_rxns } - return self.sendPgdbFnCallList('pathways-of-compound', may_be_frameid(cpd), **kwargs) - - def deactivated_or_inhibited_by_compound(self, cpds, mode=None, mechanisms=None, phys_relevant=None, slots=None): - """ - Description - Returns all pathways in which the given compound appears as a - substrate. - Parms - cpds - An instance or list of instances of class Compounds, a frame id or PFrame. - mode - Keyword, Represents the type of regulation. Can - take on the values of "+", "-", or None. - mechanisms - Keyword, Keywords from the mechanism slot of - the corresponding sub-class of the class Regulation. If - True, only regulation objects with mechanisms in this - list will be explored for regulated objects. - phys_relevant - Keyword, If True, then only return inhibitors - that are associated with Regulation instances that have - the physiologically-relevant? slot set to True. - slots - Keyword, A list of enzymatic reaction slots. - - Return value - A list of instances of class Enzymatic-Reactions. - """ - kwargs = {'mode': mode, - 'mechanisms': mechanisms, - 'phys-relevant?': phys_relevant, - 'slots': slots } - return self.sendPgdbFnCallList('deactivated-or-inhibited-by-compound', may_be_frameid(cpds), **kwargs) - - def tfs_bound_to_compound(self, cpd, include_inactive=None): - """ - Description - Returns a list of protein complexes that, when bound to the - given compound, act as a transcription factor. - Parms - cpd - An instance of class Compounds, a frame id or PFrame. - include_inactive - Keyword, If True, then the inactive form of - the protein is also checked. See the function - transcription-factor? for more information. - - Return value - A list of instances of class Proteins. - """ - kwargs = {'include-inactive?': include_inactive} - return self.sendPgdbFnCallList('tfs-bound-to-compound', may_be_frameid(cpd), **kwargs) - - - def get_name_string(self, item, rxn_eqn_as_name=None, rxn_common_name_as_name=None, - direction=None, name_slot=None, strip_html=None, - include_species_strain_name=None, - italicize_species=None, short_name=None, - species_initials=None, primary_class=None): - """ - Description - Given an object, compute the string name. The method used to - compute the name varies per the object class. - Parms - item - A frame id or PFrame. - rxn_eqn_as_name - Keyword, If True, then we use the reaction - equation in string form as the name of the reaction. - Defaults to True. - rxn_common_name_as_name - Keyword, If True, then we use the reaction's - common name as the name of the reaction. - direction - Keyword, An argument of 'l2r' or 'r2l' can be - given to specify the desired reaction orientiation when - printed in reaction equation form. If this is not provided, - then the reaction direction will be determined using pathway - evidence. - name_slot - Keyword, The specified slotunit frame name, as a - symbol, will be used for extracting the name of the frame. - strip_html - Keyword, Remove any HTML mark-up from the string - form of the object name. - include_species_strain_name - Keyword, Provide proper italicization for the - organism strain name. - italicize_species - Keyword, Provide proper italicization for the - organism species name. - short_name - Keyword, If the ABBREV-NAME slot is populated - for the frame, then its value will be used. - species_initials - Keyword, Print the name of the organism as initials. - primary_class - Keyword, Specify explicitly the primary class of - the given frame. This can be used to override the internal - reasoning of this function, and you can give a suggestion to - the function to treat the frame as another class. - - Return value - A string representing the name of the frame. - """ - kwargs = {'rxn-eqn-as-name': rxn_eqn_as_name, - 'rxn-common-name-as-name': rxn_common_name_as_name, - 'direction': direction, - 'name-slot': name_slot, - 'strip-html?': strip_html, - 'include-species-strain-name?': include_species_strain_name, - 'italicize-species?': italicize_species, - 'short-name?': short_name, - 'species-initials': species_initials, - 'primary-class': Symbol(primary_class)} - return self.sendPgdbFnCall('get-name-string', may_be_frameid(item), **kwargs) - - def full_enzyme_name(self, enzyme, use_frame_name=None, name=None, activity_names=None): - """ - Description - Compute the full name of an enzyme as the concatenation of the - common name of the protein followed by the common names of its - enzymatic reactions. Note that two enzrxns for the same enzyme - could have the same common name, so we avoid including the same - name twice. - Parms - enzyme - An instance of the class Proteins, that is, a frame id or a PFrame. - use_frame_name - Keyword, If True, then the frameid of the enzyme - instance is used in computing the enzyme name. Defaults to - True. - name - Keyword, A string that bypasses the function, and will be - returned as the value of the function. - activity_names - Keyword, A provided list of strings, that represent the - names of the known catalytic activities of enzyme. - - Return value - A string. - """ - # Parameters use_frame_name, name and activity_names are optional for the Lisp fn version. - return self.sendPgdbFnCall('full-enzyme-name', may_be_frameid(enzyme), use_frame_name, - name, activity_names) - - def enzyme_activity_name(self, enzyme, reaction=None): - """ - Description - Computes the name of an enzyme in the context of a particular - reaction. If the reaction is not provided, then we return the - full enzyme name. - - Parms - enzyme - An instance of the class Proteins, that is, a frame id or a PFrame. - reaction - Keyword, An instance of the class Reactions. - - Return value - A string. - """ - # Parameter reaction is optional for the Lisp fn version. - return self.sendPgdbFnCall('enzyme-activity-name', may_be_frameid(enzyme), may_be_frameid(reaction)) - - + """ + Please consult the the tutorial.html file under the doc directory + for an introduction on how to use this class. + """ + + def __init__(self, orgid): + """ + Once a PGDB object is created, it has been validated that the organism (orgid) + exists on the running Pathway Tools server. From that PGDB object (e.g. ecoli), + many classes of objects can be retrieved by using the attribute syntax of + Python, such as ecoli.reactions. + """ + if config._debug: + print "PGDB __init__" + self._orgid = "unknown" + self._error = False + + # All PFrame objects of the PGDB are stored in attribute _frames, keyed by their frame ids. + self._frames = {} + + # Verify that the running Pathway Tools has the PGDB (organism). + try: + r = PTools.sendQueryToPTools('(orgid-exist-p \'' + orgid + ')') + except PToolsError, msg: + raise PythonCycError('Pathway Tools was unable to verify if organism (orgid) {:s} is known in your running Pathway Tools. More specifically: {:s}'.format(orgid, msg)) + if not r: + raise PythonCycError("The organism orgid {:s} is unknown. Use pythoncyc.all_orgids() to get a list of known orgids.".format(orgid)) + self._error = True + else: + self._orgid = orgid + return None + + def __getinitargs__(self): + """ For the Pickle module. """ + return (self._orgid, ) + + def __getstate__(self): + """ For the Pickle module """ + return self.__dict__.copy() + + def __setstate__(self, dict): + """ For the Pickle module """ + self.__dict__ = dict + + def __repr__(self): + return self.__str__() + + def __str__(self): + return '' + + def __dir__(self): + return (dir(self.__class__) + self.__dict__.keys()) + + def _nb_pframes(self): + """ + Return the number of PFrame objects accessible as attributes for a PGDB object. + """ + return len(self._frames) + + def __setattr__(self, attr, val): + if attr.startswith('_'): + self.__dict__[attr] = val + return None + attrId = convertLispIdtoPythonId(attr) + if isinstance(val, PFrame): + self._frames[attrId] = val + else: + self.__dict__[attrId] = val + return None + + def __getattr__(self, attr): + """ + Attributes for a PGDB may refer to frame ids. A frame id that has dashes in + Pathway Tools, is converted to attribute with underscores '_' instead. If an + attribute does not exist yet, a request to Pathway Tools is done to verify if it + may exist as an instance or as a class. PFrame instances and classes are created + automatically when the corresponding instances or classes exist in the PGDB. + """ + if config._debug: + print "PGDB ", self._orgid, "__getattr__", attr + + # If the converted attribute exists as an attribute. + attrId = convertLispIdtoPythonId(attr) + if attrId in self.__dict__: + return self.__dict__[attrId] + if isinstance(attr,int): + return self._frames[attr] + if attrId in self._frames: + return self._frames[attrId] + + # It could be an access to a class of objects (e.g. genes -> |Genes|). + realClassName = self.is_a_class_name(attr) + if realClassName: + # Use realClassName for the frame id, not attr. + return self.get_class_data(realClassName) + + # It could be an instance in the PGDB. Try to create a frame for it. + realInstanceName = self.is_an_instance_name(attr) + if realInstanceName: + # Use the realname for the frame-id so that retrieving the + # object from Pathway Tools will work. + frame = PFrame(realInstanceName, self, getFrameData=True, isClass=False) + return frame + else: + return None + + if 'IPython' in sys.modules: + def _ipython_display_(self): + table = "" + # A PGDB frame may contain thousands of attributes, one + # for each instance. This output is too large to print in + # most cases. Print a succinct representation of the PGDB frame. + table = table + "" + table = table + "" + table = table + "
orgid" + self._orgid + "
Number of PFrames" + str(self._nb_pframes()) + "
" + display(HTML(table)) + + def __setitem__(self, attr, val): + attrId = convertLispIdtoPythonId(attr) + if isinstance(val, PFrame): + self._frames[attrId] = val + else: + self.__dict__[attrId] = val + return None + + def __getitem__(self, index): + if config._debug: + print "PGDB __getitem__", index + if (isinstance(index,int) or isinstance(index,slice)) : + if self._frames: + return self._frames[index] + else: + raise PythonCycError('This PGDB has no _frames attribute.') + + # Accessing an item such as ecoli['trp'], index is a string not a number. + if index in self._frames: + return self._frames[index] + else: + attrId = convertLispIdtoPythonId(index) + if attrId in self._frames: + return self._frames[attrId] + else: + return self.__getattr__(index) + + def __eq__(self, other): + # The name of the orgid determines the object. + if isinstance(other, PGDB): + return self._orgid == other._orgid + else: + return False + + def __ne__(self, o): + return not self.__eq__(o) + + def save_pgdb(self): + """ + Save a PGDB that has been modified in the running Pathway Tools server. The PGDB + that will be saved is based on the orgid of this PGDB object. + """ + return self.sendPgdbFnCallBool('save-kb') + + def get_major_classes(self): + """ + Get from Pathway Tools the classes Reactions, Pathways, Genes, Compounds, + Proteins, and all their instances with their data. This method is very time + consuming has several ten of thousands of frames need to be transferred from + Pathway Tools and the corresponding PFrames need to be created. + """ + self.reactions + self.pathways + self.genes + self.compounds + self.proteins + self.get_frame_objects([f.frameid for f in self.reactions.instances]) + self.get_frame_objects([f.frameid for f in self.pathways.instances]) + self.get_frame_objects([f.frameid for f in self.genes.instances]) + self.get_frame_objects([f.frameid for f in self.compounds.instances]) + self.get_frame_objects([f.frameid for f in self.proteins.instances]) + + def sendPgdbQuery(self, query): + """ + Send a query for a specific PGDB using its orgid. + Use the macro with-organism for the Lisp Python server. + + Parm + query, a string. That string should be acceptable to the Lisp Python server. + + Return + the result (as a Python object) of the execution of the query in Pathway Tools. + """ + # Evaluate a query in the context of this PGDB. + if self._orgid == "unknown": + print "Cannot send any query because the selected organism is unknown." + return None + else: + lisp_query = '(with-organism (:org-id \'' + self._orgid + ') ' + query + ')' + print lisp_query + return PTools.sendQueryToPTools(lisp_query) + + def sendPgdbFnCall(self, fn, *args, **kwargs): + """ + Send a PGDB query to Pathway Tools based on function fn and arguments args and + kwargs (keyword args) and return the result. If multiple values are + returned by fn, the Pathway Tools Python server transforms them into a list. + """ + print fn + fnCall = prepareFnCall(fn, *args, **kwargs) + return self.sendPgdbQuery(fnCall) + + def sendPgdbFnCallBool(self, fn, *args, **kwargs): + """ + Send a PGDB query to Pathway Tools that will return a Bool value. + This method takes care of translating no value or an empty list to False. + """ + result = self.sendPgdbFnCall(fn, *args, **kwargs) + if result == None or result == []: + return False + else: + return result + + def sendPgdbFnCallList(self, fn, *args, **kwargs): + """ + Send a PGDB query to Pathway Tools that will return a List value. + This method takes care of translating no value or False to an empty list. + """ + result = self.sendPgdbFnCall(fn, *args, **kwargs) + if result == None or result == False: + return [] + else: + return result + + def is_a_class_name(self, className): + """ + Verify that className is a known class in Pathway Tools. + Return the real name of that class because the className may have + been transformed by fn class-name-p to generate the closest real class name. + + Parm + className, a string, the class name to verify. + + Return + a string, either className itself, or modified by replacing + '_' to '-' or some case letters changed to match an existing class + name in Pathway Tools. + """ + return self.sendPgdbFnCallBool('class-name-p', className) + + def get_class_data(self, realClassName, getInstancesData=False): + """ + Retrieve the class slots and their values, creating a PFrame for the class. + Retrieve also the list of instances from Pathway Tools and create a PFrame for + each instance. Store the list of PFrames in attribute 'instances' of the class + object. If getInstancesData is True, get also all instances slots and their + data. + + Parms + realClassName, a string, the real name of the class to retrieve. + getInstancesData, boolean, True => get the slots and data of all instances. + + Returns + A PFrame representing the class with all its slot names + as Python attributes. + """ + fclass = PFrame(realClassName, self, getFrameData=True, isClass = True) + attrId = convertLispIdtoPythonId(realClassName) + frameids = self.sendPgdbFnCallList('get-class', fclass) + if not (frameids == None): + if getInstancesData: + # Create PFrame instances with all their slots and data. + instances = self.get_frame_objects(frameids) + else: + # Create PFrame instances but the data for each frame is not brought in now. + # Reuse a PFrame for a frameid, if it already exists for this PGDB. + instances = self.create_frame_objects(frameids) + fclass.__dict__['instances'] = instances + return fclass + + def create_frame_objects(self, frameids): + """ + Create all the required PFrames for the given frameids. If a PFrame already + exist for a frameid on the PGDB, reuse that PFrame, otherwise create a PFrame. + No data is transferred from Pathway Tools. + + Parm + frameids, list of frame ids (strings) + + Side-Effects + self is modified to contain new PFrames indexed on new frameids + + Return + list of PFrames + """ + pframes = [] + for frameid in frameids: + attrID = convertLispIdtoPythonId(frameid) + if attrID in self.__dict__: + f = self.__dict__[attrID] + else: + f = PFrame(frameid, self) + self.__dict__[attrID] = f + pframes.append(f) + return pframes + + def get_frame_objects(self, frameids): + """ + For each frame id of the list frameids, retrieve the slots + and their data. Reuse the PFrame of frameid if it already exist for this PGDB, + otherwise create one and attach it to this PGDB. + + Parm + frameids, list of frame ids (strings). + + Return + list of PFrames, one for each frame id. + """ + frameObjects = self.sendPgdbFnCallList('get-frame-objects', may_be_frameid(frameids)) + pframes = [] + for frameid, slotsData in frameObjects.iteritems(): + attrID = convertLispIdtoPythonId(frameid) + if attrID in self.__dict__: + f = self.__dict__[attrID] + else: + f = PFrame(frameid, self) + self.__dict__[attrID] = f + pframes.append(f) + f._gotframe = True + for slot, data in slotsData.iteritems(): + f.__dict__[convertLispIdtoPythonId(slot)] = data + return pframes + + def is_an_instance_name(self, frameid): + """ + Similar to method is_a_class_name but for a frame that is not a class. + If frameid is a real frame id of an object of this PGDB, returns frameid as is. + If not, try to convert frameid to an exist frame id by transforming cases of + letters and underscores to dashes in frameid. + + Parm + frameid, a string. + + Returns + a string representing an existing frame id in the PGDB. + """ + return self.sendPgdbFnCallBool('frameid-instance-p', Symbol(frameid)) + + def get_class_all_instances(self, className): + """ + Get all instances of the given class name for this PGDB. ClassName must be + exactly as Pathway Tools expect the name of the class, no conversion is applied. + + Parm + className, a symbol specified as a string (e.g., '|Reactions|') + + Returns + list of frameids + """ + return self.sendPgdbFnCallList('gcai', Symbol(className)) + + def get_class_all_subs(self, classArg): + """ + Get all subclasses of the given class name for this PGDB. If classArg is a + string, it must be exactly as Pathway Tools expect the name of the class, no + conversion is applied. + + Parm + classArg, a symbol specified as a string (e.g., '|Reactions|') or as a PFrame. + + Returns + list of frameids corresponding to the subclasses of the classArg. + """ + return self.sendPgdbFnCallList('get-class-all-subs', classArg) + + def run_fba(self, fileName): + """ + In PythonCyc, there is a run_fba method defined globally in the pythoncyc module + and there is this version which is run under a specific PGDB. Notice, though, + that the FBA input file provided will decide which organism is used for running + FBA and may override this PGDB. + + Parms + fileName + a string which is the name of the FBA input file on the running + Pathway Tools machine. + + Returns + A list with the following positional values: + 1) True <=> success, the FBA completed without error (for growth, see 5) + 2) List of error messages, if any + 3) List of output messages generated by MetaFlux (FBA module) during parsing + and execution + 4) The solver (SCIP) status symbol + 5) The flux of the objective biomass, non-zero if growth + 6) Number of growth cases if FBA input file is a knockout run, + or the number of active reactions if the FBA input file is solving a model + 7) The list of reactions that were in the model after instantiation + 8) The list of reactions that were active (non zero flux) with their fluxes + """ + return self.sendPgdbFnCall('python-run-fba', fileName) + + def get_slot_values(self, frameid, slotName): + """ + Return the slot values of a frame object. + + Parms + frameid + a string representing the unique identifier for a frame object. + slotName + a string representing the slot of the frame object. + + Returns + list of values of the given slot. Values can be frameids, booleans, + strings, or numbers. + + Example: + To get the substrates participating on the left of reaction RXN-9000: + meta.get_slot_values('RXN-9000', 'LEFT') + where meta is a variable bound to a PGDB object. + """ + return self.sendPgdbFnCallList('get-slot-values', Symbol(frameid), Symbol(slotName)) + + def put_slot_values(self, frameid, slotName, val): + """ + Modify the slot values of a frame object with the given val. Val is typically + a list of objects. + + Important: + The modified frame is not updated for any PFrame object that might has been + previously loaded from that PGDB. This operation should be used only for its + effect on the PGDB in the running Pathway Tools application. + + Parms + frameid + a string representing the unique identifier for a frame object. + slotName + a string representing the slot of the frame object. + val + a value to store in the slot, typically a list of values or objects. + + Side-Effects + The slot of that frame is replaced with the new value. + + Returns + Nothing + + Example: + To put the substrates participating on the left of reaction RXN-9000: + put_slot_values('RXN-9000', 'LEFT', ['CPD-9459','CPD-9460']) + """ + return self.sendPgdbFnCallList('put-slot-values', Symbol(frameid), Symbol(slotName), val) + + def put_slot_value(self, frameid, slotName, val): + """ + Modify the slot value of a frame object with the given val. Val is a single + value (e.g., not a list). + + Important: + The modified frame is not updated for any PFrame object that might has been + previously loaded from that PGDB. This operation should be used only for its + effect on the PGDB in the running Pathway Tools application. + + Parms + frameid + a string representing the unique identifier for a frame object. + slotName + a string representing the slot of the frame object. + val + a value to store in the slot. + + Side-Effects + The slot of that frame is replaced with the new value + + Returns + Nothing + + Example: + To put the Gibbs free energy of reaction RXN-9000: + put_slot_value('RXN-9000', 'GIBBS-0', 7.52) + """ + return self.sendPgdbFnCall('put-slot-value', Symbol(frameid), Symbol(slotName), val) + + def get_slot_value(self, frameid, slotName): + """ + Return the single slot value of a frame object. + + Parms + frameid + a string representing the unique identifier for a frame object. + slotName + a string representing the slot of the frame object. + + Example: + To get the substrates participating on the left of reaction RXN-9000: + get_slot_values('RXN-9000', 'LEFT') + """ + return self.sendPgdbFnCall('get-slot-value', Symbol(frameid), Symbol(slotName)) + + # Section 5.1 Enumeration operations + def all_pathways(self, selector='all', base=False): + """ + Description + Returns a list of pathway instance frames of a specified type. + + Parms + selector + Selects whether all pathways, or just small-molecule metabolism base pathways. + Can take either 'all' or 'small-molecule'. Defaults to 'all'. + base + If this boolean parameter is True, only includes base pathways. Otherwise, all + pathways, including superpathways, will be returned. + + Return value + A list of instances of class Pathways. + """ + return self.sendPgdbFnCallList('all-pathways', mkey(selector), base) + + def all_reactions(self, type_of_reactions='metab-smm'): + """ + Description + same as all_rxns() + """ + return self.all_rxns(type_of_reactions) + + def all_rxns(self, type_of_reactions='metab-smm'): + """ + Description + Returns a set of reactions that fall within a particular category. + + Parms + type_of_reactions + The type of reaction to return. Defaults to 'metab-smm'. + + The possible values are: + 'all' + All reactions. + 'protein-small-molecule-reaction' + One of the substrates of the reaction is a + macromolecule, and one of the substrates of the reaction + is a small molecule. + 'protein-reaction' + All substrates of the reaction are proteins. + 'trna-reaction' + One of the substrates of the reaction is a tRNA. + 'spontaneous' + Spontaneous reactions. + 'spontaneous-ht' + 'enzyme' + All enzyme-catalyzed reactions (i.e., instances of + either EC-Reactions class or Unclassified-Reactions class). + 'enzyme-ht' + 'small-molecule' + All reactions whose substrates are all small molecules, + as opposed to macromolecules. Excludes transport reactions. + 'small-molecule-ht' + 'metab-pathways' + All reactions found within metabolic pathways. Includes + reactions that are pathway holes. May include a handfull + of reactions whose substrates are macromolecules, e.g., + ACP. Excludes transport reactions. + 'all-rxns-metab-pathways-with-duplicates-ht' + 'metab-smm' + All reactions of small molecule metabolism, whether or + not they are present in a pathway. Subsumes + metab-pathways. + 'smm' + 'metab-smm-ht' + 'metab-complete-smm' + 'metab-all' + All enzyme-catalyzed reactions. Subsumes metab-smm. + 'transport-ht' + 'transport' + All transport reactions. + 'enzyme-not-in-pwy' + + Return value + A list of reaction frame ids. + """ + return self.sendPgdbFnCallList('all-rxns', mkey(type_of_reactions)) + + def all_substrates(self, rxns): + """ + Description + Returns all unique substrates used in the reactions specified by + the parameter rxns. + Parms + rxns + A list of reaction PFrames or frame ids. + + Return value + A list of compound frame ids. There might be strings in the list, + as the left and right slots of a reaction frame can contain strings. + """ + return self.sendPgdbFnCallList('all-substrates', may_be_frameid(rxns)) + + def all_cofactors(self): + """ + Description + Return a list of all cofactors used in the current PGDB. + + Return value + A list of cofactor frame ids. + """ + return self.sendPgdbFnCallList('all-cofactors') + + def all_modulators(self): + """ + Description + Enumerate all of the modulators, or direct regulators, in the + current PGDB. + + Return value + A list of regulator frame ids. + """ + return self.sendPgdbFnCallList('all-modulators') + + def all_sigma_factors(self): + """ + Description + Enumerate all RNA polymerase sigma factors. + + Return value + A list of all instances of the class Sigma-Factors. + """ + return self.sendPgdbFnCallList('all-sigma-factors') + + def all_operons(self): + """ + Description + Enumerates all operons. In this case, an operon is defined as a + list of overlapping instances of Transcription-Units. + + Return value + A list of lists of Transcription-Units, where all + Transcription-Units in the list belong to the same operon. + """ + return self.sendPgdbFnCallList('all-operons') + + def all_transporters(self): + """ + Description + Enumerate all transport proteins. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('all-transporters') + + def all_transported_chemicals(self, from_compartment=None, to_compartment=None, show_compartment=None, primary_only=False): + """ + Description + Enumerates all chemicals transported by transport reactions in + the current PGDB. + + Parms + from_compartment + Keyword, The compartment that the chemical is + coming from (see Cellular Component Ontology). + to_compartment + Keyword, The compartment that the chemical is + going to (see Cellular Component Ontology). + primary_only + Keyword, If True, filter out common transport + compounds, such as protons and Na+. + + Return value + A list of compound frame ids. + """ + kwargs = { + 'from-compartment' : may_be_frameid(from_compartment), + 'to-compartment' : may_be_frameid(to_compartment), + 'show-compartment' : may_be_frameid(show_compartment), + 'primary-only?' : primary_only + } + return self.sendPgdbFnCallList('all-transported-chemicals', **kwargs) + + def all_protein_complexes(self, filter='all'): + """ + Description + Enumerates different types of protein complexes. + + Parms + filter + Keyword, The type of protein complexes to return. + + The argument must be one of the following values: + 'all' + Return all protein complexes. + 'hetero' + Return all heteromultimers. + 'homo' + Return all homomultimers. + + Return value + A list of protein complex frame ids. + """ + kwargs = { + 'filter' : mkey(filter) + } + return self.sendPgdbFnCallList('all-protein-complexes', **kwargs) + + def all_transcription_factors(self, allow_modified_forms=True): + """ + Description + Enumerates all transcription factors, or just unmodified forms + of transcription factors. + + Parms + allow_modified_forms + Keyword, A boolean value. If True, modified and unmodified forms of the protein + are returned. If false, then only unmodified forms of the proteins are returned. + The default value is True. + + Return value + A list of protein frame ids that are transcription factors. + """ + kwargs = { + 'allow-modified-forms?' : allow_modified_forms + } + return self.sendPgdbFnCallList('all-transcription-factors', **kwargs) + + def all_genetic_regulation_proteins(self, allow_modified_forms=True, class_name=None): + """ + Description + Enumerates all proteins that are involved in genetic regulation + of a particular given class. Optionally, just unmodified forms + of the proteins are returned. + + Parms + class_name + Keyword, The class Regulation or a subclass. + It defaults to Regulation-of-Transcription-Initiation. + allow_modified_forms + Keyword, A boolean value. If True, modified and + unmodified forms of the protein are returned. If false, then + only unmodified forms of the proteins are returned. The + default value is True. + + Return value + A list of protein frames that are involved in the specified form + of regulation. + """ + kwargs = { + 'allow-modified-forms?' : allow_modified_forms, + 'class' : Symbol(class_name) + } + return self.sendPgdbFnCallList('all-genetic-regulation-proteins', **kwargs) + + def rxns_w_isozymes(self, rxns=None): + """ + Description + Enumerate all reactions that have isozymes (distinct proteins or + protein classes that catalyze the same reaction). + + Parms + rxns + Keyword, A list of instances of the class Reactions. + Defaults to the result of (all-rxns :enzyme). + + Return value + A list of A list of instances of the class Reactions with isozymes. + """ + kwargs = { + 'rxns' : may_be_frameid(rxns) + } + return self.sendPgdbFnCallList('rxns-w-isozymes', **kwargs) + + def rxns_catalyzed_by_complex(self, rxns=None): + """ + Description + Enumerates all reactions catalyzed by an enzyme that is a protein complex. + + Parms + rxns + Keyword, A list of instances of the class Reactions. + Defaults to the result of (all-rxns :enzyme). + + Return value + A list of instances of the class Reactions with a protein + complex as an enzyme. + """ + kwargs = { + 'rxns' : may_be_frameid(rxns) + } + return self.sendPgdbFnCallList('rxns-catalyzed-by-complex', **kwargs) + + def all_enzymes(self, type_of_reactions=None): + """ + Description + Return all enzymes of a given type. + + Parm + type_of_reactions + Keyword, A type as taken from the parameter to + fn enzyme. Defaults to 'chemical-change'. + + Return value + A list of instances of class Proteins. + """ + kwargs = { + 'type' : type_of_reactions + } + return self.sendPgdbFnCallList('all-enzymes', **kwargs) + + # Section 5.1.1 Operations on Reactions + def genes_of_reaction(self, rxn): + """ + Description + Return all genes that encode the enzymes of a given reaction. + + Parms + rxn, An instance of the class Reactions, a frame id or PFrame. + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('genes-of-reaction', may_be_frameid(rxn)) + + def substrates_of_reaction(self, rxn): + """ + Description + Return all of the reactants and products of a given reaction. + + Parms + rxn, An instance of the class Reactions, a frame id or PFrame. + + Return value + A list that may consist of children of class Compounds, + children of class Polymer-Segments, or strings. + """ + return self.sendPgdbFnCallList('substrates-of-reaction', may_be_frameid(rxn)) + + def enzymes_of_reaction(self, rxn, species=None, experimental_only=None, local_only_p=None): + """ + Description + Return the enzymes that catalyze a given reaction. + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + species + Keyword, A list of species, such that in a + multi-organism PGDB such as MetaCyc, only proteins found in + those organisms will be returned. This list can include + valid org-ids, children of class Organisms, and + strings. Please see the documentation for the species + slot-unit for more information. Default value is nil. + experimental_only + Keyword, When True, only return enzymes that have + a non-computational evidence code associated with it. + local_only_p + Keyword, When True, only return enzymes that + catalyze the specific form of the reaction, as opposed to + enzymes that are known to catalyze a more general form + (i.e., class) of the reaction. + + Return value + A list of children of class Proteins or class + Protein-RNA-Complexes. + """ + + kwargs = { + 'species' : species, + 'experimental-only?' : experimental_only, + 'local-only-p' : local_only_p + } + return self.sendPgdbFnCallList('enzymes-of-reaction', may_be_frameid(rxn), **kwargs) + + def reaction_reactants_and_products(self, rxn, direction=None, pwy=None): + """ + Description + Return the reactants and products of a reaction, based on a specified direction. + The direction can be specified explicity or by giving a pathway as an argument. + It is an error to both specify the pathway and the explicit direction. If + neither an explicit direction or a pathway is given as an argument, then the + direction is computationally inferred from available evidence within the PGDB. + + Parms + rxn + An instance of the class Reactions, that is, a frame id or PFrame. + direction + Keyword, Can take on the following values: + 'L2R' + The reaction direction goes from 'left to right', as + described in the Reactions instance. + 'R2L' + The reaction direction goes from 'right to left'; the + opposite of what is described in the Reactions + instance. + pwy + Keyword, An instance of the class Pathways, a frame id or PFrame. + + Return value + Returns multiple values as a list. The first value is a list of reactants as + determined by the direction of the reaction, and the second value is a list of + the products as determined by the direction of the reaction. Both lists have + items that are children of class Compounds, children of class Polymer-Segments, + or strings. + """ + kwargs = { + 'direction' : direction, + 'pwy' : may_be_frameid(pwy) + } + return self.sendPgdbFnCall('reaction-reactants-and-products', may_be_frameid(rxn), **kwargs) + + def reaction_type(self, rxn): + """ + Description + Returns a keyword describing the type of reaction. + + Parms + rxn, An instance of the class Reactions, a frame id or PFrame. + + Return value + A string from the following list: + 'small-molecule' + All substrates are small molecules, or small-molecule classes. + 'transport' + A substrate is marked with different compartment annotations + in the left and right slots. + 'protein-small-molecule-reaction' + At least one substrate is a protein and at least one is a + small molecule. + 'protein-reaction' + All substrates are proteins. + 'trna-reaction' + At least one substrate is a tRNA. + 'null-reaction' + No substrates or reactants are specified. + 'other' + None of the preceding cases apply. + """ + return self.sendPgdbFnCall('reaction-type', may_be_frameid(rxn)) + + def rxn_without_sequenced_enzyme_p(self, rxn): + """ + Description + A predicate that tests if a given reaction has genes with no + associated sequence information. + Parms + rxn + An instance of the class Reactions, that is, a frame id or PFrame. + complete + Keyword, if True, the predicate will return True when there + is any associated gene without a sequence. If False, the + predicate will return True when all associated genes are + without a sequence. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('reaction-without-sequenced-enzyme-p', may_be_frameid(rxn)) + + def pathway_hole_p(self, rxn): + """ + Description + A predicate that determines if the current reaction is + considered to be a 'pathway hole', or without an associated enzyme. + + Parms + rxn, An instance of the class Reactions, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('pathway-hole-p', may_be_frameid(rxn)) + + def rxn_present_p(self, rxn, include_spontaneous=None): + """ + Description + A predicate that determines if there is evidence for the + occurrence of the given reaction in the current PGDB. + + Parms + rxn, An instance of the class Reactions, that is, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('rxn-present?', may_be_frameid(rxn)) + + def rxn_specific_form_of_rxn_p(self, specific_rxn, generic_rxn): + """ + Description + A predicate that is True if the given generic reaction is a + generalized form of the given specific reaction. + + Parms + specific_rxn + A child of the class Reactions, that is, a frame id or PFrame. + generic_rxn + A child of the class Reactions, that is, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('rxn-specific-form-of-rxn-p', may_be_frameid(specific_rxn), may_be_frameid(generic_rxn)) + + def nonspecific_forms_of_rxn(self, rxn): + """ + Description + Return all of the generic forms of the given specific reaction. + Not every reaction will necessarily have a generic form. + + Parms + rxn, An instance of the class Reactions, that is, a frame id or PFrame. + + Return value + A list of children of the class Reactions. + """ + return self.sendPgdbFnCallList('nonspecific-forms-of-rxn', may_be_frameid(rxn)) + + def specific_forms_of_rxn(self, rxn): + """ + Description + Return all of the specific forms of the given generic reaction. + Not every reaction will necessarily have a specific form. + + Parms + rxn, A child of the class Reactions, that is, a frame id or PFrame. + + Return value + A list of instances of the class Reactions. + """ + return self.sendPgdbFnCallList('specific-forms-of-rxn', may_be_frameid(rxn)) + + def rxn_in_compartment_p(self, rxn, compartments, default_ok=None, pwy=None, loose=None): + """ + Description + A predicate that checks if the given reaction is present in a + list of cellular compartments. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + compartments + A list of cellular compartments, as defined in the Cellular + Components Ontology. See frame CCO. + default_ok + Keyword, If True, then we return True if the + reaction has no associated compartment information, or one + of its associated locations is a super-class of one of the + members of the compartments parameter. + pwy + Keyword, a frame id or PFrame. + If supplied, the search for associated + enzymes of the parameter rxn is limited to the given child + of Pathways. + loose + Keyword, boolean. If True, then the compartments + CCO-CYTOPLASM and CCO-CYTOSOL are treated as being the + same compartment. + + Return value + A boolean value. + """ + kwargs = { + 'default-ok?' : default_ok, + 'pwy' : may_be_frameid(pwy), + 'loose' : loose + } + return self.sendPgdbFnCallBool('rxn-in-compartment-p', may_be_frameid(rxn), compartments, **kwargs) + + def compartment_of_rxn(self, rxn, default=None): + """ + Description + Returns the compartment of the reaction for non-transport + reactions. + + Parms + rxn + An instance of the class Reactions, that is, a frame id or PFrame. + default + Keyword, The default compartment for reactions without any + compartment annotations on their substrates. The default + value is CCO-CYTOSOL. + + Return value + A child of the class Cell Compartment Ontology. + """ + return self.sendPgdbFnCall('compartment-of-rxn', may_be_frameid(rxn)) + + def compartments_of_reaction(self, rxn, sides=None, default_compartment=None): + """ + Description + Returns the compartments associated with the given reaction. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + sides + Keyword, The slots of the reaction to consider. + The default value is (LEFT RIGHT). + default_compartment + Keyword, + The default compartment, as determined by the function + (default-compartment), which currently is set to + CCO-CYTOSOL. + + Return value + A list of children of the class CCO. + """ + kwargs = { + 'sides' : sides, + 'default-compartment' : may_be_frameid(default_compartment) + } + return self.sendPgdbFnCallList('compartments-of-reaction', may_be_frameid(rxn), **kwargs) + + def transported_chemicals(self, rxn, side=None, primary_only=None, from_compartment=None, to_compartment=None, show_compartment=None): + """ + Description + Return the compounds in a transport reaction that change + compartments. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + side + Keyword, The side of the reaction from which to + return the transported compound. + primary_only + Keyword, If True, then filter out common + exchangers (currently defined as (PROTON NA CPD-1)+). If + True, and the only transported compounds are in this list, + then the filter doesn't apply. + from_compartment + Keyword, A compartment (child of class CCO). + If specified, then only return compounds transported from + that compartment. + to_compartment + Keyword, A compartment (child of class CCO). + If specified, then only return compounds transported to that + compartment. + show_compartment + Keyword, A compartment (child of class CCO). + If specified, and the compound is modified during transport, + then only return the form of the compound as found in this + compartment. + + Return value + A list of children of class Compounds. + """ + kwargs = { + 'side' : side, + 'primary-only?' : primary_only, + 'from-compartment' : may_be_frameid(from_compartment), + 'to-compartment' : may_be_frameid(to_compartment), + 'show-compartment' : may_be_frameid(show_compartment) + } + return self.sendPgdbFnCallList('transported-chemicals', may_be_frameid(rxn), **kwargs) + + def get_predecessors(self, rxn, pwy): + """ + Description + Return a list of all reactions that are direct predecessors + (i.e., occurr earlier in the pathway) of the given reaction in + the given pathway. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + pwy + A child of the class Pathways. + + Return value + A list of instances of the class Reactions. + """ + return self.sendPgdbFnCallList('get-predecessors', may_be_frameid(rxn), may_be_frameid(pwy)) + + def get_successors(self, rxn, pwy): + """ + Description + Return a list of all reactions that are direct successors (i.e., + occurr later in the pathway) of the given reaction in the given + pathway. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + pwy + A child of the class Pathways. + + Return value + A list of instances of the class Reactions. + """ + return self.sendPgdbFnCallList('get-successors', may_be_frameid(rxn), may_be_frameid(pwy)) + + def rxn_w_isozymes_p(self, rxn): + """ + Description + A predicate that tests if a given reaction has any associated + isozymes (distinct proteins or protein classes that catalyze the + same reaction). + + Parms + rxn, An instance of the class Reactions, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('rxn-w-isozymes-p', may_be_frameid(rxn)) + + # Section 5.1.2 Operations on Pathways + def genes_of_pathway(self, pwy, sorted=None): + """ + Description + Return all genes coding for enzymes in the given pathway. + + Parms + pwy + An instance of the class Pathways, a frame id or PFrame. + sorted? + Keyword, If True, the genes are sorted in the + order in which the corresponding reaction occurrs in the + sequence of the pathway. + + Return value + A list of instances of class Genes. + """ + kwargs = { + 'sorted?' : sorted + } + return self.sendPgdbFnCallList('genes-of-pathway', may_be_frameid(pwy), **kwargs) + + def enzymes_of_pathway(self, pwy, species=None, experimental_only=None, sorted=None): + """ + Description + Return all enzymes that are present in the given pathway. + Parms + + pwy + An instance of the class Pathways, a frame id or PFrame. + species + Keyword, A list of species, such that in a + multi-organism PGDB such as MetaCyc, only proteins found in + those organisms will be returned. This list can include + valid org-ids, children of class Organisms, and + strings. Please see the documentation for the species + slot-unit for more information. + experimental_only + Keyword, When True, only return enzymes that have + a non-computational evidence code associated with it. + sorted + Keyword, If True, the enzymes are sorted in the + order in which the corresponding reaction occurrs in the + sequence of the pathway. + + Return value + A list of children of class Proteins or class + Protein-RNA-Complexes. + """ + kwargs = { + 'species' : species, + 'experimental-only?' : experimental_only, + 'sorted?' : sorted + } + return self.sendPgdbFnCallList('enzymes-of-pathway', may_be_frameid(pwy), **kwargs) + + def compounds_of_pathway(self, pwy): + """ + Description + Return all substrates of all reactions that are within the given + pathway. + + Parms + pwy, An instance of the class Pathways, a frame id or PFrame. + + Return value + A list of children of class Compounds, children of class + Polymer-Segments, or strings. + """ + return self.sendPgdbFnCallList('compounds-of-pathway', may_be_frameid(pwy)) + + def substrates_of_pathway(self, pwy): + """ + Description + Bearing in mind the direction of all reactions within a pathway, this function + returns the substrates of the reactions in four groups: a list of all reactant + compounds (compounds occurring on the left side of some reaction in the given + pathway), the list of proper reactants (the subset of reactants that are not + also products), a list of all products, and a list of all proper products. + + Parms + pwy, An instance of the class Pathways, a frame id or PFrame. + + Return value + Four values as a list, each of which is a list of substrates. A substrate + may be a child of class Compounds, a child of class Polymer-Segments, or a string. + """ + return self.sendPgdbFnCall('substrates-of-pathway', may_be_frameid(pwy)) + + def variants_of_pathway(self, pwy): + """ + Description + Returns all variants of a pathway. + + Parms + pwy, An instance of the class Pathways, a frame id or PFrame. + + Return value + A list of instance of the class Pathways. + """ + return self.sendPgdbFnCallList('variants-of-pathway', may_be_frameid(pwy)) + + def pathway_components(self, pwy, rxn_list=None, pred_list=None): + """ + Description + Returns all of the connected components of a pathway. A connected component of a + pathway is a set of reactions in the pathway such that for all reactions R1 in + the connected component, a predecessor relationship holds between R1 and some + other reaction R2 in the connected component, and each connected component is of + maximal size. Every pathway will have from 1 to N connected components, where N + is the number of reactions in the pathway. Most pathways have one connected + component, but not all. + + Parms + pwy, a frame id or PFrame. + An instance of the class Pathways, which is not a + super-pathway (i.e., does not have any entries in its + sub-pathways slot). + rxn_list + Keyword, The list of reactions to use as the starting list + of connected component clusters. Defaults to + the content of slot reaction-list in pwy. + pred_list + Keyword, The list of reaction predecessors to iterate from + in order to cluster the reactions in rxn-list. Defaults to + list in slot predecessors of pwy. + + Return value + Returns three values as a list: the connected components as a list of + lists of the form ((r1 r2 r3) (r4 r5) (r6 r7 r8)) where each + sub-list contains all reactions in one connected component, the + number of connected components, and the length of the reaction + list. + """ + kwargs = { + 'rxn-list' : may_be_frameid(rxn_list), + 'pred-list': may_be_frameid(pred_list) + } + return self.sendPgdbFnCall('pathway-components', may_be_frameid(pwy), **kwargs) + + def noncontiguous_pathway_p(self, pwy): + """ + Description + A predicate that determines if the pathway contains more than + one connected component. See function pathway-components for + more explanation. + + Parms + pwy, An instance of the class Pathways, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('noncontiguous-pathway-p', may_be_frameid(pwy)) + + def rxns_adjacent_in_pwy_p(self, rxn1, rxn2, pwy): + """ + Description + A predicate to determine if two given reactions are adjacent to + one another in the given pathway. + + Parms + rxn1 + An instance of the class Reactions, a frame id or PFrame. + rxn2 + An instance of the class Reactions, a frame id or PFrame. + pwy + An instance of the class Pathways, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('rxns-adjacent-in-pwy-p', may_be_frameid(rxn1), may_be_frameid(rxn2), may_be_frameid(pwy)) + + # Section 5.1.3 Operations on Enzymatic-Reactions + def cofactors_and_pgroups_of_enzrxn(self, enzrxn): + """ + Description + Returns the cofactors and prosthetic groups of an enzymatic + reaction. + + Parm + enzrxn, An instance of the class Enzymatic-Reactions, a frame id or PFrame. + + Return value + A list of children of class Chemicals or strings, representing + cofactors and/or prosthetic groups. + """ + return self.sendPgdbFnCallList('cofactors-and-pgroups-of-enzrxn', may_be_frameid(enzrxn)) + + def enzrxn_activators(self, enzrxn, phys_relevant_only=None): + """ + Description + Returns the list of activators (generally small molecules) of + the enzymatic reaction frame. + + Parms + enzrxn + An instance of the class Enzymatic-Reactions, a frame id or PFrame. + phys_relevant_only + Keyword, If True, then only return activators that are + associated with Regulation instances that have the + physiologically-relevant? slot set to True. + + Return value + A list of children of the class Chemicals. + """ + # phys_relevant_only is optional for the Lisp version + return self.sendPgdbFnCallList('enzrxn-activators', may_be_frameid(enzrxn), phys_relevant_only) + + def enzrxn_inhibitors(self, enzrxn, phys_relevant_only=None): + """ + Description + Returns the list of inhibitors (generally small molecules) of + the enzymatic reaction frame. + + Parms + enzrxn + An instance of the class Enzymatic-Reactions, a frame id or PFrame. + phys_relevant_only + Keyword, If True, then only return inhibitors that are + associated with Regulation instances that have the + physiologically-relevant? slot set to True. + + Return value + A list of children of the class Chemicals. + """ + # phys_relevant_only is optional for the Lisp version + return self.sendPgdbFnCallList('enzrxn-inhibitors', may_be_frameid(enzrxn), phys_relevant_only) + + def pathways_of_enzrxn(self, enzrxn, include_super_pwys=None): + """ + Description + Returns the list of pathways in which the given enzymatic + reaction participates. + + Parms + enzrxn + An instance of the class Enzymatic-Reactions, a frame id or PFrame. + include_super_pwys + Keyword, If True, then not only will the + direct pathways in which enzrxn is associated in be + returned, but also any enclosing super-pathways. If enzrxn + is associated with a reaction that is directly associated + with a super-pathway, then the function might return + super-pathways even if this option is nil. + + Return value + A list of instances of class Pathways. + """ + kwargs = { + 'include-super-pwys?' : include_super_pwys + } + return self.sendPgdbFnCallList('pathways-of-enzrxn', may_be_frameid(enzrxn), **kwargs) + + def pathway_allows_enzrxn(self, pwy, rxn, enzrxn, single_species=None): + """ + Description + A predicate which returns a True value if the given pathway + allows the given enzymatic reaction to catalyze the given + reaction. Certain pathways have a list of enzymatic reactions + that are known not to catalyze certain reactions. See the + documentation of slot-unit enzyme-use for more information. + + Parms + pwy + An instance of the class Pathways, a frame id or PFrame. + rxn + An instance of the class Reactions, a frame id or PFrame. + enzrxn + An instance of the class Enzymatic-Reactions, a frame id or PFrame. + single_species + Keyword, An instance of the class Organisms If set, + then enzrxn has the further constraint that it must be an + enzymatic reaction present in the organism specified by the + value passed to single-species. + + Return value + A boolean value. + """ + # single_species is optional for the Lisp version. + # TODO + return self.sendPgdbFnCallBool('pathway-allows-enzrxn?', may_be_frameid(pwy), may_be_frameid(rxn), may_be_frameid(enzrxn), single_species) + + # Section 5.1.4 Operations on Proteins + def monomers_of_protein(self, protein, coefficients=None, unmodify=None): + """ + Description + Returns the monomers of the given protein complex. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + coefficients + Keyword, If True, then the second return value of + the function will be a list of monomer coefficients. + Defaults to True. + unmodify + Keyword, If True, obtain the monomers of the + unmodified form of p. + + Return value + First value is a list of instances of the class Proteins. If + coefficients? is True, then the second value is the + corresponding coefficients of the monomers fromthe first return + value. + """ + kwargs = { + 'coefficients?' : coefficients, + 'unmodify?' : unmodify + } + return self.sendPgdbFnCallList('monomers-of-protein', may_be_frameid(protein), **kwargs) + + def base_components_of_protein(self, protein, exclude_small_molecules=None): + """ + Description + Same as function monomers-of-protein, but also returns + components of the protein that are RNAs or compounds, not just + polypeptides. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + exclude_small_molecules + Keyword, If nil, then small molecule components + are also returned. Default value is True. + + Return value + Two values as a list. The first value is a list of the components, which + can be instances of the following classes: Polypeptides, + RNA, and Compounds. The second value is a list of the + corresponding coefficients of the components in the first value. + """ + kwargs = {'exclude-small-molecules?': exclude_small_molecules} + return self.sendPgdbFnCall('base-components-of-protein', may_be_frameid(protein), **kwargs) + + def containers_of(self, protein, exclude_self=None): + """ + Description + Return all complexes of which the given protein is a direct or indirect component. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + exclude_self + Keyword, If True, then protein will not be included in + the return value. + + Return value + A list of instances of the class Proteins. + """ + # exclude_self is an optional parameter for the Lisp fn version. + return self.sendPgdbFnCallList('containers-of', may_be_frameid(protein), exclude_self) + + def protein_or_rna_containers_of(self, protein, exclude_self=None): + """ + Description + This function is the same as the function containers-of, except that it only + includes containers that are instances of either class Protein-Complexes, or + class Protein-RNA-Complexes. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + exclude_self + Keyword, If True, then protein will not be included in + the return value. + + Return value + A list of instances of the class Proteins. + """ + # exclude_self is an optional parameter for the Lisp fn version. + return self.sendPgdbFnCallList('protein-or-rna-containers-of', may_be_frameid(protein), exclude_self) + + def homomultimeric_containers_of(self, protein, exclude_self=None): + """ + Description + This function is the same as the function containers-of, + except that it only includes containers that are homomultimers. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + exclude_self + Keyword, If True, then protein will not be included in + the return value. + + Return value + A list of instances of the class Proteins. + """ + # exclude_self is an optional parameter for the Lisp fn version. + return self.sendPgdbFnCallList('homomultimeric-containers-of', may_be_frameid(protein), exclude_self) + + def polypeptide_or_homomultimer_p(self, protein): + """ + Description + A predicate that determines if the given protein is a + polypeptide or a homomultimer. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('polypeptide-or-homomultimer-p', may_be_frameid(protein)) + + def unmodified_form(self, protein): + """ + Description + Return the unmodified form of the given protein, which might be + the same as the given protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + An instance of the class Proteins. + """ + return self.sendPgdbFnCall('unmodified-form', may_be_frameid(protein)) + + def unmodified_or_unbound_form(self, protein): + """ + Description + Return the unmodified form or unbound (to a small molecule) form + of the given protein, which might be the same as the given protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + An instance of the class Proteins. + """ + return self.sendPgdbFnCall('unmodified-or-unbound-form', may_be_frameid(protein)) + + def reduce_modified_proteins(self, prots, debind=None): + """ + Description + Given a list of proteins, the function converts all of the + proteins to their unmodified form, and then removes any + duplicates from the subsequent list. + + Parms + prots + A list of instances of the class Proteins, a frame id or PFrame. + debind + Keyword, When True, the proteins are further + simplified by obtaining the unbound form of the protein, if + it is bound to a small molecule. + + Return Value + A list of instances of the class Proteins. + """ + kwargs = { + 'debind?' : debind + } + if isinstance(prots, list): + return self.sendPgdbFnCallList('reduce-modified-proteins', may_be_frameid(prots), **kwargs) + else: + return self.sendPgdbFnCallList('reduce-modified-proteins', may_be_frameid([prots]), **kwargs) + + def all_direct_forms_of_protein(self, protein): + """ + Description + Given a protein, this function will return all of the directly + related proteins of its modified and unmodified forms, meaning + all of their direct subunits and all of their direct containers. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return Value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('all-direct-forms-of-protein', may_be_frameid(protein)) + + def all_forms_of_protein(self, protein): + """ + Description + Given a protein, this function will return all of the related + proteins of its modified and unmodified forms, meaning all of + their subunits and all of their containers. Unlike + all_direct_forms_of_protein, this function is not limited to + the direct containers only. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('all-forms-of-protein', may_be_frameid(protein)) + + def modified_forms(self, protein, exclude_self=None, all_variants=None): + """ + Description + Returns all modified forms of a protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + exclude_self + Keyword, If True, then protein will not be included in + the return value. + all_variants + Keyword, If True, and protein is a modified form, then + we return all of the modified forms of the unmodified forms + of protein. + + Return value + A list of instances of the class Proteins. + """ + # Parameters exclude_self and all_variants are optionals for the Lisp fn version. + return self.sendPgdbFnCallList('modified-forms', may_be_frameid(protein), exclude_self, all_variants) + + def modified_and_unmodified_forms(self, protein): + """ + Description + Returns all of the modified and unmodified forms of the given + protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('modified-and-unmodified-forms', may_be_frameid(protein)) + + def modified_containers(self, protein): + """ + Description + Returns all containers of a protein (including itself), and all + modified forms of the containers. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('modified-containers', may_be_frameid(protein)) + + def top_containers(self, protein): + """ + Description + Return the top-most containers (i.e., they are not a component + of any other protein complex) of the given protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('top-containers', may_be_frameid(protein)) + + def small_molecule_cplxes_of_prot(self, protein): + """ + Description + Return all of the forms of the given protein that are complexes + with small molecules. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('small-molecule-cplxes-of-prot', may_be_frameid(protein)) + + def genes_of_protein(self, protein): + """ + Description + Given a protein, return the set of genes which encode all of the + monomers of the protein. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Genes. + """ + return self.sendPgdbFnCallList('genes-of-protein', may_be_frameid(protein)) + + def genes_of_proteins(self, prots): + """ + Description + The same as genes_of_protein, except that it takes a list of + proteins and returns a set of genes. + + Parms + prots + A list of instances of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Genes. + """ + if isinstance(prots, list): + return self.sendPgdbFnCallList('genes-of-proteins', may_be_frameid(prots)) + else: + return self.sendPgdbFnCallList('genes-of-proteins', may_be_frameid([prots])) + + def reactions_of_enzyme(self, protein, kb=None, include_specific_forms=None, include_subreactions=None): + """ + Description + Return all of the reactions associated with a given protein via + enzymatic reactions. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + kb + Keyword, The KB object of the KB in which to find + the associated reactions. Defaults to self. + include_specific_forms + Keyword, When True, specific forms of associated + generic reactions are also returned. Default value is True. + + Return value + A list of instances of the class Reactions. + """ + kwargs = { + 'kb' : kb, + 'include-specific-forms?' : include_specific_forms, + 'include-subreactions?' : include_subreactions + } + return self.sendPgdbFnCallList('reactions-of-enzyme', may_be_frameid(protein), **kwargs) + + def species_of_protein(self, protein): + """ + Description + Get the associated species for the given protein. + + Parms + protein + A list of instances of the class Proteins, a frame id or PFrame. + + Return value + An instance of the class Organisms, or a string. + """ + return self.sendPgdbFnCall('species-of-protein', may_be_frameid(protein)) + + def enzyme_p(self, protein, type_of_reactions=None): + """ + Description + Predicate that determines whether a specified protein is an + enzyme or not. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + type_of_reactions + Keyword, Can take on one of the following values to select + more precisely what is meant by an "enzyme": + + 'any' + Any protein that catalyzes a reaction is considered an + enzyme. + 'chemical-change' + If the reactants and products of the catalyzed reactin + differ, and not just by their cellular location, then + the protein is considered an enzyme. + 'small-molecule' + If the reactants of the catalyzed reaction differ and + are small molecules, then the protein is considered an + enzyme. + 'transport' + If the protein catalyzes a transport reaction. + 'non-transport' + If the protein only catalyzes non-transport reactions. + 'non-transport-non-pathway' + If the protein only catalyzes non-transport reactions and + it is not present in any pathway + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('enzyme-p', may_be_frameid(protein), mkey(type_of_reactions)) + + def leader_peptide_p(self, protein): + """ + Description + A predicate that determines whether the given protein is a + leader peptide. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('leader-peptide?', may_be_frameid(protein)) + + def protein_p(self, frame): + """ + Description + A predicate that determines whether the given frame is a protein. + + Parms + frame + a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('protein-p', may_be_frameid(frame)) + + def complex_p(self, frame): + """ + Description + A predicate that determines whether the given frame is a + protein complex. + + Parms + frame + a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('complex-p', may_be_frameid(frame)) + + def reactions_of_protein(self, protein, check_protein_components=None, check_protein_containers=None): + """ + Description + Returns all of the associated reactions that the given protein, + or its components, catalyzes. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + check_protein_components? + Keyword, If True, check all components of this protein for + catalyzed reactions. Defaults to True. + check_protein_containers? + Keyword, If True, check the containers and modified forms + of the protein for catalyzed reactions. + + Return value + A list of instances of class Reactions. + """ + return self.sendPgdbFnCallList('reactions-of-protein', may_be_frameid(protein), check_protein_components, check_protein_containers) + + def protein_in_compartment_p(self, rxn, compartments, default_ok=None, pwy=None, loose=None): + """ + Description + A predicate that checks if the given reaction is present in a + list of cellular compartments. + + Parms + rxn + An instance of the class Reactions, a frame id or PFrame. + compartments + A list of cellular compartments, as defined in the Cellular + Components Ontology. See frame CCO. + default_ok + Keyword, If True, then we return True if the + reaction has no associated compartment information, or one + of its associated locations is a super-class of one of the + members of the compartments parameter. + pwy + Keyword, a frame id or PFrame. If supplied, the search for associated + enzymes of the parameter rxn is limited to the given child + of Pathways. + loose + Keyword, If True, then the compartments CCO-CYTOPLASM and CCO-CYTOSOL + are treated as being the same compartment. + + Return value + A boolean value. + """ + kwargs = { + 'default-ok?' : default_ok, + 'pwy' : may_be_frameid(pwy), + 'loose?': loose + } + return self.sendPgdbFnCallBool('protein-in-compartment-p', may_be_frameid(rxn), may_be_frameid(compartments), **kwargs) + + def all_transporters_across(self, membranes=None, method=None): + """ + Description + Returns a list of transport proteins that transport across one + of the given membranes. + Parms + membranes + Keyword, Either :all or a list of instances of the class membranes. + Defaults to :all (CCO-MEMBRANE). + method + Keyword, + Either 'location' or 'reaction-compartments'. 'location' + will check the locations slot, while + 'reaction-compartments' will examine the compartments of + reaction substrates. Default value is 'location'. + + Return value + A list of instances of class Proteins. + """ + kwargs = { + #'membranes' : may_be_frameid(membranes), + 'membranes' : mkey(membranes), + 'method': method + } + return self.sendPgdbFnCallList('all-transporters-across', **kwargs) + + def autocatalytic_reactions_of_enzyme(self, protein): + """ + Description + Returns a list of reaction frames, where the protein + participates as a substrate of the reaction, and the reaction + has no associated Enzymatic Reaction frame. This implies that + the protein substrate of the reaction might autocatalyzing the + reaction. + + Parms + protein + An instance frame of class Proteins, a frame id or PFrame. + + Return value + A list of instances of class Reactions. + """ + return self.sendPgdbFnCallList('autocatalytic-reactions-of-enzyme', may_be_frameid(protein)) + + # Section 5.1.5 Operations on Genes + def gene_p(self, gene): + """ + Description + A predicate to determine if the given frame is a gene. + + Parms + gene + a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('gene-p', may_be_frameid(gene)) + + def enzymes_of_gene(self, gene): + """ + Description + Collects all of the enzymes encoded by the given gene, including + modified forms and complexes in which it is a sub-component. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('enzymes-of-gene', may_be_frameid(gene)) + + def all_products_of_gene(self, gene): + """ + Description + Collects all proteins (not necessarily enzymes) that are encoded + by the given gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('all-products-of-gene', may_be_frameid(gene)) + + def reactions_of_gene(self, gene): + """ + Description + Returns all reactions catalyzed by enzymes encoded by the given + gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + A list of instances of class Reactions. + """ + return self.sendPgdbFnCallList('reactions-of-gene', may_be_frameid(gene)) + + def pathways_of_gene(self, gene, include_super_pwys=None, include_gene_prod_as_substrate=None): + """ + Description + Returns the pathways of enzymes encoded by the given gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + include_super_pwys + Keyword, If True, then not only will the + direct pathways in which gene encodes an enzyme be + returned, but also any enclosing super-pathways. If gene + is associated with a reaction that is directly associated + with a super-pathway, then the function might return + super-pathways even if this option is nil. + + Return value + A list of instances of class Pathways. + """ + kwargs = { + 'include-super-pwys?' : include_super_pwys, + 'include-gene-prod-as-substrate?' : include_gene_prod_as_substrate + } + return self.sendPgdbFnCallList('pathways-of-gene', may_be_frameid(gene), **kwargs) + + def chromosome_of_gene(self, gene): + """ + Description + Returns the replicon on which the gene is located. If the gene + is located on a contig that is, in turn, part of a chromosome, + then the contig is returned. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + An instance of class Genetic-Elements. + """ + return self.sendPgdbFnCall('chromosome-of-gene', may_be_frameid(gene)) + + def unmodified_gene_product(self, gene): + """ + Description + Returns the first element of the list returned by the function + unmodified-gene-products. This is useful if you are sure that + there are no alternative splice forms of your gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + An instance of either class Polypeptides or 'RNA. + """ + return self.sendPgdbFnCall('unmodified-gene-product', may_be_frameid(gene)) + + def unmodified_gene_products(self, gene): + """ + Description + Return all of the unmodified gene products (i.e. alternative + splice forms) of the given gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + A list of instances of either class Polypeptides or 'RNA. + """ + return self.sendPgdbFnCallList('unmodified-gene-products', may_be_frameid(gene)) + + def next_gene_on_replicon(self, gene): + """ + Description + Return the next gene on the replicon. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + Returns two values as a list. The first value is the next gene, or nil if + there is not a next gene (i.e., the gene is at the end of a + linear replicon). The second value is 'last' if the gene is the + last gene on a linear replicon. + """ + return self.sendPgdbFnCall('next-gene-on-replicon', may_be_frameid(gene)) + + def previous_gene_on_replicon(self, gene): + """ + Description + Return the previous gene on the replicon. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + Returns two values as a list. The first value is the previous gene, or nil + if there is not a previous gene (i.e., the gene is at the + beginning of a linear replicon). The second value is 'first' if + the gene is the first gene on a linear replicon. + """ + return self.sendPgdbFnCall('previous-gene-on-replicon', may_be_frameid(gene)) + + def adjacent_genes_p(self, g1, g2): + """ + Description + Given two genes, this predicate will return True if they are on + the same replicon, and adjacent to one another. + Parms + g1 + An instance of class Genes, a frame id or PFrame. + g2 + An instance of class Genes, a frame id or PFrame. + + Return value + A list if genes are in the same replicon. Otherwise False. + """ + if g1 == g2: + print "genes are the same." + return None + else: + return self.sendPgdbFnCallBool('adjacent-genes?', may_be_frameid(g1), may_be_frameid(g2)) + + def neighboring_genes_p(self, g1, g2, max_gap=10): + """ + Description + Given two genes, this predicate determines if the two genes are + "neighbors", or within a certain number of genes from one + another along the replicon. + Parms + g1 + An instance of class Genes, a frame id or PFrame. + g2 + An instance of class Genes, a frame id or PFrame. + max_gap + Keyword, An integer representing the number of genes g1 + and g2 can be from one another. Default value is 10. + + Return value + A boolean value. + """ + if g1 == g2: + print "genes are the same." + return None + else: + return self.sendPgdbFnCallBool('neighboring-genes-p', may_be_frameid(g1), may_be_frameid(g2), max_gap) + + def gene_clusters(self, genes, max_gap=10): + """ + Description + Groups together genes based on whether each gene is a gene + neighbor with other genes. + + Parms + genes + A list of instances of class Genes, a frame id or PFrame. + max_gap + Keyword, An integer representing the number of genes any + pair from genes can be from one another. Default value is 10. + + Return value + A dictionary of lists if genes are located below max_gap, where the key is a + gene from genes, and the value is a list with all of the gene neighbors of the + first gene. Otherwise returns an empty list. + """ + return self.sendPgdbFnCallList('gene-clusters', may_be_frameid(genes), max_gap) + + def rna_coding_gene(self, gene): + """ + Description + A predicate that determines if the given gene encodes an RNA. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('rna-coding-gene?', may_be_frameid(gene)) + + def protein_coding_gene(self, gene): + """ + Description + A predicate that determines if the given gene encodes a protein + (as opposed to an RNA). + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCall('protein-coding-gene?', may_be_frameid(gene)) + + def pseudo_gene_p(self, gene): + """ + Description + A predicate that determines if the given gene is a pseudo-gene. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('pseudo-gene-p', may_be_frameid(gene)) + + def phantom_gene_p(self, gene): + """ + Description + A predicate that determines if the given gene is a phantom gene. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('phantom-gene-p', may_be_frameid(gene)) + + def dna_binding_site_p(self, gene): + """ + Description + A predicate that determines if the given frame is an instance of + the class DNA-Binding-Sites. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('dna-binding-site-p', may_be_frameid(gene)) + + def terminator_p(self, gene): + """ + Description + A predicate that determines if the given object is an instance + of the class Terminators. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('terminatorp', may_be_frameid(gene)) + + def operon_of_gene(self, gene): + """ + Description + Given a gene, return a list of transcription units that form the + operon containing the gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame + + Return value + A list of instances of class Transcription-Units. + """ + return self.sendPgdbFnCallList('operon-of-gene', may_be_frameid(gene)) + + def genes_in_same_operon(self, gene): + """ + Description + Given a gene, return all other genes in the same operon. + + Parms + gene + An instance of class Genes, a frame id or PFrame. + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('genes-in-same-operon', may_be_frameid(gene)) + + def gene_transcription_units(self, gene): + """ + Description + Given a gene, return all of the transcription units which + contain the gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame + + Return value + A list of instances of class Transcription-Units. + """ + return self.sendPgdbFnCallList('gene-transcription-units', may_be_frameid(gene)) + + def cotranscribed_genes(self, gene): + """ + Description + Return all co-transcribed genes (i.e., genes which are a part of + one or more of the same transcription units) of the given gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('cotranscribed-genes', may_be_frameid(gene)) + + def terminators_affecting_gene(self, gene): + """ + Description + Find terminators in the same transcription unit and upstream of + the given gene. + + Parms + gene + An instance of class Genes, a frame id or PFrame + + Return value + A list of instances of class Terminators. + """ + return self.sendPgdbFnCallList('terminators-affecting-gene', may_be_frameid(gene)) + + def chromosome_of_object(self, item): + """ + Description + Given a frame object, the replicon where it is located is returned. If there is + no associated replicon for the object, nil is returned. If the object is on more + than one replicon, an error is thrown. + + Parms + item, a frame id or PFrame + An instance of class All-Genes, Transcription-Units, + Promoters, Terminators, Misc-Features, or + DNA-Binding-Sites. + + Return value + An instance of class Genetic-Elements. + """ + return self.sendPgdbFnCall('chromosome-of-object', may_be_frameid(item)) + + # Section 5.1.6 Operations on Regulation Frames + def activation_p(self, reg_frame): + """ + Description + A predicate that determines if a given regulation frame is + describing activation. + + Parms + reg_frame + An instance of class Regulation, a frame id or PFrame + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('activation-p', may_be_frameid(reg_frame)) + + def inhibition_p(self, reg_frame): + """ + Description + A predicate that determines if a given regulation frame is + describing inhibition. + Parms + reg_frame + An instance of class Regulation, a frame id or PFrame + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('inhibition-p', may_be_frameid(reg_frame)) + + def direct_regulators(self, item, filter_fn=None): + """ + Description + Return all regulators that are connected to a regulated object + by a single regulation object. + + Parms + item + A frame id or PFrame. + filter_fn + Keyword, A predicate used to filter the regulation objects + used to find the regulators. + + Return value + A list of frames that regulate item. + """ + kwargs = { + 'filter-fn' : filter_fn + } + return self.sendPgdbFnCallList('direct-regulators', may_be_frameid(item), **kwargs) + + def direct_activators(self, item): + """ + Description + Return all activators that are connected to an activated object + by a single regulation object. + + Parms + item + A frame id or PFrame. + + Return value + A list of frames that activate item. + """ + return self.sendPgdbFnCallList('direct-activators', may_be_frameid(item)) + + def direct_inhibitors(self, item): + """ + Description + Return all inhibitors that are connected to an inhibited object + by a single regulation object. + + Parms + item + A frame id or PFrame. + + Return value + A list of frames that inhibit item. + """ + return self.sendPgdbFnCallList('direct-inhibitors', may_be_frameid(item)) + + def transcription_factor_p(self, protein, include_inactive=None): + """ + Description + A predicate that determines if the given protein is a + transcription factor, or a component of a transcription factor. + + Parms + protein + An instance frame of class Proteins, a frame id or PFrame. + include_inactive + Keyword, If True, then the function checks to see + if any of its components or containers is a transcription + factor as well. + + Return value + A boolean value. + """ + kwargs = { + 'include-inactive?' : include_inactive + } + return self.sendPgdbFnCallBool('transcription-factor?', may_be_frameid(protein), **kwargs) + + def regulator_of_type(self, protein, class_name): + """ + Description + A predicate that determines if the given protein is a regulator + of the specified class. + + Parms + protein + An instance frame of class Proteins, a frame id or PFrame. + class + A subclass of Regulation. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('regulator-of-type?', may_be_frameid(protein), class_name) + + def regulon_of_protein(self, protein): + """ + Description + Returns all transcription units regulated by any form of the + given protein. + + Parms + protein + An instance frame of class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Transcription-Units. + """ + return self.sendPgdbFnCallList('regulon-of-protein', may_be_frameid(protein)) + + def regulation_frame_transcription_units(self, reg_frame): + """ + Description + Given a regulation object, return the transcription units when + one of the regulated entities is a promoter or terminator of the + transcription unit. + + Parms + reg_frame + An instance of the class Regulation-of-Transcription, a frame id or PFrame. + + Return value + A list of instances of the class Transcription-Units. + """ + return self.sendPgdbFnCallList('regulation-frame-transcription-units', may_be_frameid(reg_frame)) + + def transcription_unit_regulation_frames(self, tu): + """ + Description + Returns a list of regulation frames that regulate the transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of the class Regulation. + """ + return self.sendPgdbFnCallList('transcription-unit-regulation-frames', may_be_frameid(tu)) + + def transcription_unit_activation_frames(self, tu): + """ + Description + Returns a list of regulation frames that activate the transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of the class Regulation. + """ + return self.sendPgdbFnCallList('transcription-unit-activation-frames', may_be_frameid(tu)) + + def transcription_unit_inhibition_frames(self, tu): + """ + Description + Returns a list of regulation frames that inhibit the transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of the class Regulation. + """ + return self.sendPgdbFnCallList('transcription-unit-inhibition-frames', may_be_frameid(tu)) + + def transcription_units_of_protein(self, protein): + """ + Description + Return all of the transcription units for which the given + protein, or its modified form, acts as a regulator. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Transcription-Units. + """ + return self.sendPgdbFnCallList('transcription-units-of-protein', may_be_frameid(protein)) + + def genes_regulated_by_protein(self, protein): + """ + Description + Return all of the genes for which the given protein, or its + modified form, acts as a regulator. + + Parms + protein + An instance of the class Proteins, a frame id or PFrame. + + Return value + A list of instances of the class Genes. + """ + return self.sendPgdbFnCallList('genes-regulated-by-protein', may_be_frameid(protein)) + + def DNA_binding_sites_of_protein(self, tf, all_forms=None): + """ + Description + Given a transcription factor, return all of its DNA binding sites. + + Parms + tf + An instance of the class Proteins, a frame id or PFrame. + all_forms + Keyword, When True, then return the DNA binding + sites of modified forms and subunits of tf as well. + + Return value + A list of instances of the class DNA-Binding-Sites. + """ + kwargs = { + 'all-forms?' : all_forms + } + return self.sendPgdbFnCallList('DNA-binding-sites-of-protein', may_be_frameid(tf), **kwargs) + + def regulator_proteins_of_transcription_unit(self, tu): + """ + Description + Returns all transcription factors that regulate the given + transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('regulator-proteins-of-transcription-unit', may_be_frameid(tu)) + + def transcription_factor_ligands(self, tfs, mode): + """ + Description + For a single transcription factor or list of transcription + factors, return all transcription factor ligands. + + Parms + tfs, a frame id or PFrame or a list of these. + An instance or a list of instances of the class + Proteins. If tfs is not the active form, then the + active form is determined automatically. + mode + One of the following values: 'activator', 'inhibitor', or + 'both'. + + Return value + A list of instances of the class Chemicals or strings. + """ + return self.sendPgdbFnCallList('transcription-factor-ligands', may_be_frameid(tfs), mkey(mode)) + + def transcription_factor_active_forms(self, tfs): + """ + Description + For a given transcription factor, find all active forms (i.e, + form of the protein that regulates) of the transcription factor. + + Parms + tfs, a frame id or PFrame. An instance of the class Proteins. + + Return value + A list of instances of the class Proteins. + """ + return self.sendPgdbFnCallList('transcription-factor-active-forms', may_be_frameid(tfs)) + + def genes_regulating_gene(self, gene): + """ + Description + Return all genes regulating the given gene by means of a + transcription factor. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('genes-regulating-gene', may_be_frameid(gene)) + + def genes_regulated_by_gene(self, gene): + """ + Description + Return all genes regulated by the given gene by means of a + transcription factor. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('genes-regulated-by-gene', may_be_frameid(gene)) + + def regulators_of_gene_transcription(self, gene, by_function=None): + """ + Description + Returns a list of proteins that are regulators of the given gene. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + by_function + Keyword, If True, then return two values: a list of + activator proteins and a list of inhibitor proteins. + + Return value + A list of instances of class Proteins. If by_function is + True, then two values are returned. The first value is a list + of activator proteins, and the second value is a list of + inhibitor proteins. + """ + kwargs = { + 'by-function?' : by_function + } + return self.sendPgdbFnCall('regulators-of-gene', may_be_frameid(gene), **kwargs) + + def transcription_unit_activators(self, tu): + """ + Description + Returns all activator proteins of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('transcription-unit-activators', may_be_frameid(tu)) + + def transcription_unit_inhibitors(self, tu): + """ + Description + Returns all inhibitor proteins of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('transcription-unit-inhibitors', may_be_frameid(tu)) + + def regulators_of_operon_transcription(self, operon, by_function=None): + """ + Description + Returns a list of transcription factors of an operon. + + Parms + operon + An instance or list of instances of the class Transcription-Units, a frame id or PFrame. + by_function + Keyword, If True, then return two values: a list of + activator proteins and a list of inhibitor proteins. + + Return value + A list of instances of class Proteins. If the modified form + of the protein is the transcription factor, then that is the + protein returned. + """ + # Parameter by_function is optional for the Lisp fn. + if isinstance(operon, list): + return self.sendPgdbFnCallList('regulators-of-operon-transcription', may_be_frameid(operon), by_function) + else: + return self.sendPgdbFnCallList('regulators-of-operon-transcription', may_be_frameid([operon]), by_function) + + def transcription_unit_promoter(self, tu): + """ + Description + Returns the promoter of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + An instance of class Promoters. + """ + return self.sendPgdbFnCall('transcription-unit-promoter', may_be_frameid(tu)) + + def transcription_unit_genes(self, tu): + """ + Description + Returns the genes of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class Genes. + """ + return self.sendPgdbFnCallList('transcription-unit-genes', may_be_frameid(tu)) + + def transcription_unit_first_gene(self, tu): + """ + Description + Returns the first gene of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + An instance of class Genes. + """ + return self.sendPgdbFnCall('transcription-unit-first-gene', may_be_frameid(tu)) + + def transcription_unit_binding_sites(self, tu): + """ + Description + Returns the binding sites of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class DNA-Binding-Sites. + """ + return self.sendPgdbFnCallList('transcription-unit-binding-sites', may_be_frameid(tu)) + + def transcription_unit_transcription_factors(self, tu): + """ + Description + Returns the binding sites of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class DNA-Binding-Sites. + """ + return self.sendPgdbFnCallList('transcription-unit-transcription-factors', may_be_frameid(tu)) + + def transcription_unit_mrna_binding_sites(self, tu): + """ + Description + Returns the mRNA binding sites of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class mRNA-Binding-Sites. + """ + return self.sendPgdbFnCallList('transcription-unit-mrna-binding-sites', may_be_frameid(tu)) + + def chromosome_of_operon(self, tu): + """ + Description + Returns the replicon of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + An instance of class Genetic-Elements. + """ + return self.sendPgdbFnCall('chromosome-of-operon', may_be_frameid(tu)) + + def binding_sites_affecting_gene(self, gene): + """ + Description + Returns all binding sites which are present in the same + transcription units as the given gene. + + Parms + gene + An instance of the class Genes, a frame id or PFrame. + + Return value + A list of instances of class DNA-Binding-Sites. + """ + return self.sendPgdbFnCallList('binding-sites-affecting-gene', may_be_frameid(gene)) + + def binding_site_to_regulators(self, binding_site): + """ + Description + Returns all of the transcription factors of the given binding site. + + Parms + binding_site + An instance of class DNA-Binding-Sites, a frame id or PFrame. + + Return value + A list of instances of class Proteins. + """ + return self.sendPgdbFnCallList('binding-site->regulators', may_be_frameid(binding_site)) + + def transcription_units_of_promoter(self, promoter): + """ + Description + Returns all transcription units of a given promoter. + + Parms + promoter + An instance of class Promoters, a frame id or PFrame. + + Return value + A list of instances of class Transcription-Units. + """ + return self.sendPgdbFnCallList('transcription-units-of-promoter', may_be_frameid(promoter)) + + def promoter_binding_sites(self, promoter): + """ + Description + Returns all of the binding sites associated with the given + promoter, across multiple transcription units. + + Parms + promoter + An instance of class Promoters, a frame id or PFrame. + + Return value + A list of instances of class DNA-Binding-Sites. + """ + return self.sendPgdbFnCallList('promoter-binding-sites', may_be_frameid(promoter)) + + def transcription_unit_terminators(self, operon): + """ + Description + Returns the terminators of the given transcription unit. + + Parms + operon + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class Terminators. + """ + return self.sendPgdbFnCallList('transcription-unit-terminators', may_be_frameid(operon)) + + def containing_tus(self, binding_site): + """ + Description + Given a site (whether a DNA binding site, a promoter, a gene, or + a terminator) along a transcription unit, return the + correspodning transcription units. + + Parms + binding_site, a frame id or PFrame. + An instance of class Transcription-Units, + mRNA-Binding-Sites, DNA-Binding-Sites, + Promoters, Genes, or Terminators. + + Return value + A list of instances of class Transcription-Units. + """ + return self.sendPgdbFnCallList('containing-tus', may_be_frameid(binding_site)) + + def containing_chromosome(self, binding_site): + """ + Description + Given a site (whether a DNA binding site, a promoter, a gene, or + a terminator) along a transcription unit, return the + correspodning regulon. + + Parms + binding_site, a frame id or PFrame. + An instance of class Transcription-Units,site + mRNA-Binding-Sites, DNA-Binding-Sites, + Promoters, Genes, or Terminators. + + Return value + An instance of class Genetic-Elements. + """ + return self.sendPgdbFnCall('containing-chromosome', may_be_frameid(binding_site)) + + def binding_site_promoters(self, tu): + """ + Description + Returns the promoters of the given DNA binding site. + + Parms + tu + An instance of the class DNA-Binding-Sites, a frame id or PFrame. + + Return value + A list of instances of class Promoters. + """ + return self.sendPgdbFnCallList('binding-site-promoters', may_be_frameid(tu)) + + def transcription_unit_all_components(self, tu): + """ + Description + Returns all components (binding sites, promoters, genes, + terminators) of the given transcription unit. + + Parms + tu + An instance of the class Transcription-Units, a frame id or PFrame. + + Return value + A list of instances of class Transcription-Units, + mRNA-Binding-Sites, DNA-Binding-Sites, Promoters, + Genes, or Terminators. + """ + return self.sendPgdbFnCallList('transcription-unit-all-components', may_be_frameid(tu)) + + def binding_site_transcription_units(self, promoter): + """ + Description + Returns all transcription units of a given binding site. + + Parms + promoter, a frame id or PFrame. + An instance of class DNA-Binding-Sites or + mRNA-Binding-Sites. + + Return value + A list of instances of class Transcription-Units. + """ + return self.sendPgdbFnCallList('binding-site-transcription-units', may_be_frameid(promoter)) + + # Section 5.1.7 Operations on Compounds + def reactions_of_compound(self, cpd, non_specific_too=None, transport_only=None, compartment=None, enzymatic=None): + """ + Description + Return all reactions in which the given compound participates as + a substrate. + + Parms + cpd + a frame id or PFrame. A child of class Compounds. + non_specific_too + Keyword, If True, returns all generic + reactions where cpd, or a parent of cpd, appears as a + substrate. + transport_only + Keyword, If True, return only transport reactions. + compartment + Keyword, If True, return only reactions within + the specified compartment. + enzymatic + Keyword, If True, return only enzymatic reactions. + + Return value + A list of children of class Reactions. + """ + kwargs = { + 'non-specific-too?' : non_specific_too, + 'transport-only?' : transport_only, + 'compartment' : compartment, + 'enzymatic?' : enzymatic + } + return self.sendPgdbFnCallList('reactions-of-compound', may_be_frameid(cpd), **kwargs) + + def substrate_of_generic_rxn(self, cpd, rxn): + """ + Description + A predicate that determines if a parent of the given compound is + a substrate of the given generic reaction. + + Parms + cpd + An instance of class Compounds, a frame id or PFrame. + rxn + An instance of class Reactions, a frame id or PFrame. + + Return value + A boolean value. + """ + return self.sendPgdbFnCallBool('substrate-of-generic-rxn?', may_be_frameid(cpd), may_be_frameid(rxn)) + + def pathways_of_compound(self, cpd, non_specific_too=None, modulators=None, phys_relevant=None, include_rxns=None): + """ + Description + Returns all pathways in which the given compound appears as a + substrate. + + Parms + cpd + An instance of class Compounds, a frame id or PFrame. + non-specific_too + Keyword, If True, returns all generic + reactions where cpd, or a parent of cpd, appears as a + substrate. + modulators + Keyword, If True, returns pathways where cpd + appears as a regulator as well. + phys-relevant + Keyword, If True, then only return inhibitors + that are associated with Regulation instances that have + the physiologically-relevant? slot set to True. + include-rxns + Keyword, If True, then return a list of + reaction-pathway pairs. + + Return value + A list of instances of class Pathways. If include-rxns? is + True, then a list of lists, where each sub-list consists of + an instance of class Reactions and an instance of class + Pathways. + """ + kwargs = { + 'non-specific-too?' : non_specific_too, + 'modulators?' : modulators, + 'phys-relevant?' : phys_relevant, + 'include-rxns?' : include_rxns} + return self.sendPgdbFnCallList('pathways-of-compound', may_be_frameid(cpd), **kwargs) + + def activated_or_inhibited_by_compound(self, cpds, mode=None, mechanisms=None, phys_relevant=None, slots=None): + """ + Description + Returns all pathways in which the given compound appears as a substrate. + + Parms + cpds + An instance or list of instances of class Compounds, a frame id or PFrame. + mode + Keyword, Represents the type of regulation. Can + take on the values of "+", "-", or None. + mechanisms + Keyword, Keywords from the mechanism slot of + the corresponding sub-class of the class Regulation. If + True, only regulation objects with mechanisms in this + list will be explored for regulated objects. + phys_relevant + Keyword, If True, then only return inhibitors + that are associated with Regulation instances that have + the physiologically-relevant? slot set to True. + slots + Keyword, A list of enzymatic reaction slots. + + Return value + A list of instances of class Enzymatic-Reactions. + """ + kwargs = { + 'mode' : mode, + 'mechanisms' : mechanisms, + 'phys-relevant?' : phys_relevant, + 'slots' : slots + } + return self.sendPgdbFnCallList('ACTIVATED-OR-INHIBITED-BY-COMPOUND', may_be_frameid(cpds), **kwargs) + + def tfs_bound_to_compound(self, cpd, include_inactive=None): + """ + Description + Returns a list of protein complexes that, when bound to the + given compound, act as a transcription factor. + + Parms + cpd + An instance of class Compounds, a frame id or PFrame. + include_inactive + Keyword, If True, then the inactive form of + the protein is also checked. See the function + transcription-factor? for more information. + + Return value + A list of instances of class Proteins. + """ + kwargs = { + 'include-inactive?' : include_inactive + } + return self.sendPgdbFnCallList('tfs-bound-to-compound', may_be_frameid(cpd), **kwargs) + + # Section 5.1.8 Object Name Manipulation Operations + def get_name_string(self, item, + rxn_eqn_as_name=None, + rxn_common_name_as_name=None, + direction=None, + name_slot=None, + strip_html=None, + include_species_strain_name=None, + italicize_species=None, + short_name=None, + species_initials=None, + primary_class=None): + """ + Description + Given an object, compute the string name. The method used to + compute the name varies per the object class. + + Parms + item + A frame id or PFrame. + rxn_eqn_as_name + Keyword, If True, then we use the reaction + equation in string form as the name of the reaction. + Defaults to True. + rxn_common_name_as_name + Keyword, If True, then we use the reaction's + common name as the name of the reaction. + direction + Keyword, An argument of 'l2r' or 'r2l' can be + given to specify the desired reaction orientiation when + printed in reaction equation form. If this is not provided, + then the reaction direction will be determined using pathway + evidence. + name_slot + Keyword, The specified slotunit frame name, as a + symbol, will be used for extracting the name of the frame. + strip_html + Keyword, Remove any HTML mark-up from the string + form of the object name. + include_species_strain_name + Keyword, Provide proper italicization for the + organism strain name. + italicize_species + Keyword, Provide proper italicization for the + organism species name. + short_name + Keyword, If the ABBREV-NAME slot is populated + for the frame, then its value will be used. + species_initials + Keyword, Print the name of the organism as initials. + primary_class + Keyword, Specify explicitly the primary class of + the given frame. This can be used to override the internal + reasoning of this function, and you can give a suggestion to + the function to treat the frame as another class. + + Return value + A string representing the name of the frame. + """ + kwargs = { + 'rxn-eqn-as-name': rxn_eqn_as_name, + 'rxn-common-name-as-name': rxn_common_name_as_name, + 'direction': direction, + 'name-slot': name_slot, + 'strip-html?': strip_html, + 'include-species-strain-name?': include_species_strain_name, + 'italicize-species?': italicize_species, + 'short-name?': short_name, + 'species-initials': species_initials, + 'primary-class': Symbol(primary_class)} + return self.sendPgdbFnCall('get-name-string', may_be_frameid(item), **kwargs) + + def full_enzyme_name(self, enzyme, use_frame_name=None, name=None, activity_names=None): + """ + Description + Compute the full name of an enzyme as the concatenation of the + common name of the protein followed by the common names of its + enzymatic reactions. Note that two enzrxns for the same enzyme + could have the same common name, so we avoid including the same + name twice. + + Parms + enzyme + An instance of the class Proteins, that is, a frame id or a PFrame. + use_frame_name + Keyword, If True, then the frameid of the enzyme + instance is used in computing the enzyme name. Defaults to + True. + name + Keyword, A string that bypasses the function, and will be + returned as the value of the function. + activity_names + Keyword, A provided list of strings, that represent the + names of the known catalytic activities of enzyme. + + Return value + A string. + """ + # Parameters use_frame_name, name and activity_names are optional for the Lisp fn version. + kwargs = { + 'use-frame-name?' : use_frame_name, + 'name' : name, + 'activity_names' : activity_names + } + + #return self.sendPgdbFnCall('full-enzyme-name', may_be_frameid(enzyme), use_frame_name, name, activity_names) + return self.sendPgdbFnCall('full-enzyme-name', may_be_frameid(enzyme), **kwargs) + + def enzyme_activity_name(self, enzyme, reaction=None): + """ + Description + Computes the name of an enzyme in the context of a particular + reaction. If the reaction is not provided, then we return the + full enzyme name. + + Parms + enzyme + An instance of the class Proteins, that is, a frame id or a PFrame. + reaction + Keyword, An instance of the class Reactions. + + Return value + A string. + """ + # Parameter reaction is optional for the Lisp fn version. + return self.sendPgdbFnCall('enzyme-activity-name', may_be_frameid(enzyme), may_be_frameid(reaction)) diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index 5560e1a..386d73a 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -22,11 +22,8 @@ """ This module handles basic operations for receiving and sending messages via a -network socket to Pathway Tools. - -No major class is defined in this file, but only toplevel functions and -some simple classes for errors handling. - +network socket to Pathway Tools. No major class is defined in this file, but +only toplevel functions and some simple classes for errors handling. """ import os @@ -37,160 +34,181 @@ import config def recvAll(s): - """ - Receive the entire message sent by Pathway Tools on socket s. - The message starts with a single character type, which is either 'A' - or 'L'. The 'A' time is used without providing a length but can take - longer to receive because it uses a timeout technique to read the entire - message. The 'L' type assumes that the length of the message, in characters, - is given on the next 10 characters as an integer. The message length is the - number of characters after these 10 characters. - - Parm - s, an open network socket. - Return - the message received on socket s as a string. - """ - - if config._debug: - print 'recvAll ...' - # Get the type of message which is one character long. - type = s.recv(1) - # print "type ", type - if type == 'A': - # The length of the message is not given, use time out approach. - return recvTimeOut(s) - elif type == 'L': - # The next 10 characters give the length. - lengthMsg = int(recvFixedLength(s, 10)) - if config._debug: - print "lengthMsg ", lengthMsg - return recvFixedLength(s, lengthMsg) - else: - # Something is broken on the server side, so - # use recv with a long timeout to try flushing - # the sent message. - return recvTimeOut(s, timeOut=5) + """ + Description + Receive the entire message sent by Pathway Tools on socket s. The message starts + with a single character type, which is either 'A' or 'L'. The 'A' time is used + without providing a length but can take longer to receive because it uses a + timeout technique to read the entire message. The 'L' type assumes that the + length of the message, in characters, is given on the next 10 characters as an + integer. The message length is the number of characters after these 10 + characters. + + Parm + s, an open network socket. + + Return + the message received on socket s as a string. + """ + if config._debug: + print 'recvAll ...' + + # Get the type of message which is one character long. + type = s.recv(1) + + # print "type ", type + if type == 'A': + # The length of the message is not given, use time out approach. + return recvTimeOut(s) + elif type == 'L': + # The next 10 characters give the length. + lengthMsg = int(recvFixedLength(s, 10)) + if config._debug: + print "lengthMsg ", lengthMsg + return recvFixedLength(s, lengthMsg) + else: + # Something is broken on the server side, so + # use recv with a long timeout to try flushing + # the sent message. + return recvTimeOut(s, timeOut=5) def sendAll(s, query): - sent_len = 0 - query_len = len(query) - while sent_len < query_len: - nb_chars = s.send(query[sent_len:]) - if nb_chars == 0: - raise PythonCycError("Connection to Pathway Tools broke while sending query %s." % query) - sent_len = sent_len + nb_chars + sent_len = 0 + query_len = len(query) + while sent_len < query_len: + nb_chars = s.send(query[sent_len:]) + if nb_chars == 0: + raise PythonCycError("Connection to Pathway Tools broke while sending query {:s}.".format(query)) + sent_len = sent_len + nb_chars def recvFixedLength(s, lengthMsg): - """ - Receive a fixed length message on socket s. - Parm - lengthMsg, an integer, which is the length in characters of the - message to receive. - Return - the message received as a string. - """ - pieces = [] - nbBytesRecv = 0 - while nbBytesRecv < lengthMsg: - piece = s.recv(min(lengthMsg - nbBytesRecv, 4096)) - if piece == '': - # Give up now because nothing was received. - return ''.join(pieces) - pieces.append(piece) - nbBytesRecv = nbBytesRecv + len(piece) - # print 'Fixed receive: ', ''.join(pieces) - return ''.join(pieces) + """ + Description + Receive a fixed length message on socket s. + + Parm + lengthMsg, an integer, which is the length in characters of the message to receive. + + Return + the message received as a string. + """ + pieces = [] + nbBytesRecv = 0 + while nbBytesRecv < lengthMsg: + piece = s.recv(min(lengthMsg - nbBytesRecv, 4096)) + if piece == '': + # Give up now because nothing was received. + return ''.join(pieces) + pieces.append(piece) + nbBytesRecv = nbBytesRecv + len(piece) + # print 'Fixed receive: ', ''.join(pieces) + return ''.join(pieces) def recvTimeOut(socket, timeOut=2): - """ - Receive a message of unknown length on socket. While receiving a message, if no - more characters are sent on socket after timeOut seconds, it is - assumed that the message has ended. Therefore, it will always, whatever the lenght - of the message, take at least timeOut seconds to execute this method. If no character - is received after 60 seconds, this method returns with an empty message. - - Parms - socket, an open network socket. - timeOut, number of seconds before timing out between fragments of the received - message. - Return - The received message, as a string, on socket. - """ - # Keep each received packet in an array. - pieces = [] - # Keep track of time between recvs. - begin = time.time() - while 1: - # If we started to get data and the timeOut occurs, - # we assume that Pathway Tools sent everything. - if pieces and time.time() - begin > timeOut: - break - elif time.time() - begin > 60: - break - # Try to receive some text. - try: - data = socket.recv(4096) - if data: - pieces.append(data) - # Reset beginning time for next recv. - begin = time.time() - else: - # Slow down in case timeOut is small. - time.sleep(0.1) - except so.error: - pass - - # Join all the pieces together. - if pieces == []: - return None - else: - return ''.join(pieces) + """ + Description + Receive a message of unknown length on socket. While receiving a message, if no + more characters are sent on socket after timeOut seconds, it is assumed that the + message has ended. Therefore, it will always, whatever the lenght of the + message, take at least timeOut seconds to execute this method. If no character + is received after 60 seconds, this method returns with an empty message. + + Parms + socket + an open network socket. + timeOut + number of seconds before timing out between fragments of the received message. + + Return + The received message, as a string, on socket. + """ + # Keep each received packet in an array. + pieces = [] + + # Keep track of time between recvs. + begin = time.time() + + while 1: + # If we started to get data and the timeOut occurs, + # we assume that Pathway Tools sent everything. + if pieces and time.time() - begin > timeOut: + break + elif time.time() - begin > 60: + break + # Try to receive some text. + try: + data = socket.recv(4096) + if data: + pieces.append(data) + # Reset beginning time for next recv. + begin = time.time() + else: + # Slow down in case timeOut is small. + time.sleep(0.1) + except so.error: + pass + + # Join all the pieces together. + if pieces == []: + return None + else: + return ''.join(pieces) # Call a PTools function synchronously for any PGDB. def sendQueryToPTools(query): - """ - Send a query to a running Pathway Tools application via a socket. - - Parm - query, a string that the Python server in Pathway Tools can evaluate. - Returns - The result of the query, as a Python object, decoded by Json. - """ - if config._debug: - print 'Sending query '+query - if config._hostname == '': - raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') - try: - s = so.socket(so.AF_INET, so.SOCK_STREAM) - # Make socket non blocking. - s.setblocking(0) - s.settimeout(360) # The query may take a long time in some cases. - s.connect((config._hostname,config._hostport)) - except so.error, msg: - raise PToolsError('Failed to create a connection to a running Pathway Tools at '+ config._hostname+ ' on port '+ str(config._hostport)+'. Make sure Pathway Tools is running with option -python. Error code: '+str(msg[0])+', error message: '+ msg[1]) - # Send, receive and close socket. - sendAll(s,query) - if config._debug: - print 'Sent '+query+' to Pathway Tools.' - response = recvAll(s) - if config._debug and len(response) < 4000: - print 'JSON Received: ', response - r = json.loads(response) - s.close() - if isinstance(r,basestring) and r.startswith(':error'): - raise PToolsError('An internal error occurred in the running Pathway Tools application: %s' % r) - else: - # Return some result. - return r + """ + Description + Send a query to a running Pathway Tools application via a socket. + + Parm + query, a string that the Python server in Pathway Tools can evaluate. + + Returns + The result of the query, as a Python object, decoded by Json. + """ + if config._debug: + print 'Sending query ' + query + + if config._hostname == '': + raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') + + try: + s = so.socket(so.AF_INET, so.SOCK_STREAM) + # Make socket non blocking. + s.setblocking(0) + s.settimeout(360) # The query may take a long time in some cases. + s.connect((config._hostname, config._hostport)) + except so.error, msg: + raise PToolsError('Failed to create a connection to a running Pathway Tools at ' + config._hostname + ' on port ' + str(config._hostport) + '. Make sure Pathway Tools is running with option -python. Error code: ' + str(msg[0]) + ', error message: ' + msg[1]) + + # Send, receive and close socket. + sendAll(s, query) + + if config._debug: + print 'Sent ' + query + ' to Pathway Tools.' + + response = recvAll(s) + if config._debug and len(response) < 4000: + print 'JSON Received: ', response + r = json.loads(response) + s.close() + + if isinstance(r, basestring) and r.startswith(':error'): + raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(r)) + else: + # Return some result. + return r class PythonCycError(Exception): - """Error generated by one of the module of PythonCyc due to an incorrect - use of its methods or functions. - """ - pass + """ + Error generated by one of the module of PythonCyc due to an incorrect + use of its methods or functions. + """ + pass class PToolsError(Exception): - """Error generated when Pathway Tools send an error due to its own Lisp execution.""" - pass + """ + Error generated when Pathway Tools send an error due to its own Lisp execution. + """ + pass diff --git a/pythoncyc/PToolsFrame.py b/pythoncyc/PToolsFrame.py index e75ad1f..4d209b4 100644 --- a/pythoncyc/PToolsFrame.py +++ b/pythoncyc/PToolsFrame.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -21,243 +21,238 @@ # ---------------------------------------------------------------------- """ - Please consult file tutorial.html under the doc directory - for an introduction on how to use this class. +Please consult file tutorial.html under the doc directory for an introduction on +how to use this class. """ import sys import config from PTools import PToolsError, PythonCycError + if 'IPython' in sys.modules: - from IPython.display import display, HTML + from IPython.display import display, HTML def convertLispIdtoPythonId(s): - """ - Convert string s such that it can be a valid Python identifier. - """ - return s.replace('-','_').replace('.','_').replace('?','_p').replace('|','').lower() + """ + Convert string s such that it can be a valid Python identifier. + """ + return s.replace('-','_').replace('.','_').replace('?','_p').replace('|','').lower() class Symbol(): - """ - This class can be used to represent Lisp symbols in PythonCyc. - For example, Symbol('trp') represents the symbol trp. It is mainly used - to ensure that some arguments of methods are interpreted as symbols and not - as strings during the translation to send a request to Pathway Tools. - """ - def __init__(self, name): - self._name = name - return None + """ + This class can be used to represent Lisp symbols in PythonCyc. For example, + Symbol('trp') represents the symbol trp. It is mainly used to ensure that some + arguments of methods are interpreted as symbols and not as strings during the + translation to send a request to Pathway Tools. + """ + def __init__(self, name): + self._name = name + return None class PFrame(): - """ - PFrame is a class to represent Pathway Tools' frames. A PFrame can - represent a class frame (e.g., Reactions) as well as an instance frame - (e.g., RXN-9000). - - The required parameters to create a PFrame are the frame id (a string) and a PGDB - object. For example, assuming that 'meta' is bound to a PGDB object, the following - create a PFrame to represent the reaction RXN-9000, - - PFrame('RXN-9000', meta) - - By default, an instance PFrame (not a class PFrame) is created. - To create a PGDB object, use class PGDB, or call method pythoncyc.so. - - IPython - ------- - - A few methods were written to display frames using HTML in IPython. - Naturally, this functionality is only defined when using IPython as a - Python interpreter. - - Please consult file tutorial.html under the doc directory for an introduction - on how to use this class. - - """ - - def __init__(self, frameid, pgdb, getFrameData=False, isClass = False): - """ - The PFrame is created assuming that the frameid is coercible to a frame in the PGDB. - In particular, the frameid string is not converted and must have the appropriate camel case. - Creation of a PFrame is done lazily when getFrameData is False but is retrieved - now when getFrameData is True. - """ - # Always store the frameid surrounded by vertical bars. - self.__dict__['frameid'] = frameid if (frameid.startswith('|') and frameid.endswith('|')) else '|'+frameid+'|' - self._isclass = isClass - if isClass: - self.__dict__['instances'] = [] - # The complete frame (the slot values) is not created by default. - self._gotframe = False - # This is the PGDB object, not the PGDB name. - self.__dict__['pgdb'] = pgdb - # Add this frame on the list of current frames for this pgdb. - pgdb.__dict__['_frames'][convertLispIdtoPythonId(frameid)] = self - # Retrieve the whole frame from Pathway Tools if requested. - # TBD: add the frame on the list of instances for the corresponding class. - if getFrameData: - self.get_frame_data() - return None - - # The following four definitions are for the pickle (or cPickle) module. - # TBD: this is work in progress. - def __getinitargs__(self): - return (self.frameid, self.pgdb) - - def __getstate__(self): - # Use a compact representation of a PFrame. - return self.vectorize_dict() - - def __setstate__(self, values): - # TBD: Use schema of this PFrame to recreate dictionary. - self.__dict__ = dict - - def vectorize_dict(self): - self.__dict__.values() - - # End of definitions for pickle. - - def __getslice__(self, i, j, stride = None): - if config._debug: - print 'PFrame __getslice__ ', i, j, stride - return self.instances[i:j:stride] - - def __getattr__(self, attr): - # Accessing a slot of the frame using attribute syntax (e.g. r.left) - if config._debug: - print 'PFrame __getattr__ ', attr - - if attr in self.__dict__: - return self.__dict__[attr] - else: - attrId = convertLispIdtoPythonId(attr) - if attrId in self.__dict__: - return self.__dict__[attrId] - - if self._gotframe: - return None - # raise PythonCycError('No slot with name %s exists for frame %s.' % (attr, self.frameid)) - else: - # Get the slot value from Pathway Tools. - self.get_frame_slot_value(attr) - if not (attrId in self.__dict__): - return None - # raise PythonCycError('No slot with name %s exists for frame %s.' % (attr, self.frameid)) - else: - return self.__dict__[attrId] - - def __getitem__(self,attr): - if config._debug: - print "PFrame __getitem__ ", attr - # The slice case is for attr = slice(i,j,s) - if (isinstance(attr,int) or isinstance(attr, slice)): - if 'instances' in self.__dict__: - return self.instances[attr] - else: - raise PythonCycError('Indexing cannot be applied because this is a PFrame which is not a vector and this PFrame has no instances attribute.') - - if attr in self.__dict__: - return self.__dict__[attr] - else: - attrId = convertLispIdtoPythonId(attr) - if attrId in self.__dict__: - return self.__dict__[attrId] - else: - return self.__getattr__(attr) - - def __dir__(self): - return (dir(self.__class__) + self.__dict__.keys()) - - def get_frame_slot_value(self, slot): - """ - Retrieve the slot data for frame from Pathway Tools. - - Return - the self PFrame, modified with the new slot with data. - """ - # FrameObject is a dictionary of slot names and values. - [slotName, value] = self.pgdb.sendPgdbFnCall('get-frame-slot-value', self.frameid, Symbol(slot)) - if not slotName: - raise PythonCycError("Slot "+slot+" does not exist for frame "+self.frameid+" from organism (orgid) "+self.pgdb._orgid) - # Modify slot name to allow Python's syntax (e.g., '_' instead of '-'). - self.__dict__[convertLispIdtoPythonId(slotName)] = value - return self - - - def get_frame_data(self): - """ - Retrieve the frame data from Pathway Tools, that is, all slots and their values - for this PFrame are retrieved and stored locally. For a class, the instances - are not retrieved by this method. Instead, use method get_class_data applied to a PGDB - object. - - Return - the self PFrame, modified with the new slots and data. - """ - # FrameObject is a dictionary of slot names and values. - frameObject = self.pgdb.sendPgdbFnCall('get-frame-object', self.frameid) - if not frameObject: - raise PythonCycError("Could not retrieve frame "+self.frameid+" from organism (orgid) "+self.pgdb._orgid) - else: - self._gotframe = True - # Modify slot names to allow Python's syntax (e.g., '_' instead of '-'). - for slot in frameObject: - self.__dict__[convertLispIdtoPythonId(slot)] = frameObject[slot] - return self - - def __setattr__(self, attr, val): - if not attr.startswith('_'): - raise PythonCycError("PFrames are read only objects. Attributes of PFrame objects cannot be modified "+str((self.frameid,attr,val))+". You can only modify slot frames for the PGDB in the running Pathway Tools by using methods put_slot_value or put_slot_values using a PGDB object.") - self.__dict__[attr] = val - return None - - def __setitem__(self, attr, val): - if not attr.startswith('_'): - raise PythonCycError("PFrames are read only objects. Attributes of PFrame objects cannot be modified "+str((self.frameid,attr,val))+". You can only modify slot frames for the PGDB in the running Pathway Tools by using methods put_slot_value or put_slot_values using a PGDB object.") - self.__dict__[attr] = val - return None - - def __str__(self): - if self._isclass: - return '' - else: - return '' - - def __repr__(self): - if self._isclass: - return self.__str__() - else: - return str(self.__dict__) - - if 'IPython' in sys.modules: - def _ipython_display_(self): - table = '' - if not self._isclass: - for attr in sorted(self.__dict__): - if not (attr.startswith('_')): - table = table+""+str(attr)+""+str(self.__dict__[attr])+"" - else: - table = table+'Class '+self.frameid+' has '+str(self._nb_pframes())+' instances' - if table == '': - table = '' + self.__str__() + '' - table = ''+ table + '
' - display(HTML(table)) - - def _nb_pframes(self): - return len(self.instances) - - def __eq__(self, frame): - # If the given frame is a string, it is assumed to be a frameid. - if isinstance(frame, str): - return self.frameid == frame - # Otherwise it could be a Frame. - elif isinstance(frame, PFrame): - # TBD: should we consider the name of the pgdb? - return (self.pgdb == frame.pgdb) and (self.frameid == frame.frameid) - # Otherwise it cannot be equal to this object. - else: return False - - def __ne__(self, frame): - return not self.__eq__(frame) - - + """ + PFrame is a class to represent Pathway Tools' frames. A PFrame can represent a + class frame (e.g., Reactions) as well as an instance frame (e.g., RXN-9000). + + The required parameters to create a PFrame are the frame id (a string) and a + PGDB object. For example, assuming that 'meta' is bound to a PGDB object, the + following create a PFrame to represent the reaction RXN-9000, + + PFrame('RXN-9000', meta) + + By default, an instance PFrame (not a class PFrame) is created. + To create a PGDB object, use class PGDB, or call method pythoncyc.so. + + IPython + ------- + + A few methods were written to display frames using HTML in IPython. Naturally, + this functionality is only defined when using IPython as a Python interpreter. + + Please consult file tutorial.html under the doc directory for an introduction on + how to use this class. + """ + + def __init__(self, frameid, pgdb, getFrameData=False, isClass = False): + """ + The PFrame is created assuming that the frameid is coercible to a frame in the + PGDB. In particular, the frameid string is not converted and must have the + appropriate camel case. Creation of a PFrame is done lazily when getFrameData is + False but is retrieved now when getFrameData is True. + """ + # Always store the frameid surrounded by vertical bars. + self.__dict__['frameid'] = frameid if (frameid.startswith('|') and frameid.endswith('|')) else '|'+frameid+'|' + self._isclass = isClass + if isClass: + self.__dict__['instances'] = [] + # The complete frame (the slot values) is not created by default. + self._gotframe = False + # This is the PGDB object, not the PGDB name. + self.__dict__['pgdb'] = pgdb + # Add this frame on the list of current frames for this pgdb. + pgdb.__dict__['_frames'][convertLispIdtoPythonId(frameid)] = self + # Retrieve the whole frame from Pathway Tools if requested. + # TBD: add the frame on the list of instances for the corresponding class. + if getFrameData: + self.get_frame_data() + return None + + # The following four definitions are for the pickle (or cPickle) module. + # TBD: this is work in progress. + def __getinitargs__(self): + return (self.frameid, self.pgdb) + + def __getstate__(self): + # Use a compact representation of a PFrame. + return self.vectorize_dict() + + def __setstate__(self, values): + # TBD: Use schema of this PFrame to recreate dictionary. + self.__dict__ = dict + + def vectorize_dict(self): + self.__dict__.values() + + # End of definitions for pickle. + + def __getslice__(self, i, j, stride = None): + if config._debug: + print 'PFrame __getslice__ ', i, j, stride + return self.instances[i:j:stride] + + def __getattr__(self, attr): + # Accessing a slot of the frame using attribute syntax (e.g. r.left) + if config._debug: + print 'PFrame __getattr__ ', attr + + if attr in self.__dict__: + return self.__dict__[attr] + else: + attrId = convertLispIdtoPythonId(attr) + if attrId in self.__dict__: + return self.__dict__[attrId] + + if self._gotframe: + return None + # raise PythonCycError('No slot with name %s exists for frame %s.' % (attr, self.frameid)) + else: + # Get the slot value from Pathway Tools. + self.get_frame_slot_value(attr) + if not (attrId in self.__dict__): + return None + # raise PythonCycError('No slot with name %s exists for frame %s.' % (attr, self.frameid)) + else: + return self.__dict__[attrId] + + def __getitem__(self,attr): + if config._debug: + print "PFrame __getitem__ ", attr + # The slice case is for attr = slice(i,j,s) + if (isinstance(attr,int) or isinstance(attr, slice)): + if 'instances' in self.__dict__: + return self.instances[attr] + else: + raise PythonCycError('Indexing cannot be applied because this is a PFrame which is not a vector and this PFrame has no instances attribute.') + + if attr in self.__dict__: + return self.__dict__[attr] + else: + attrId = convertLispIdtoPythonId(attr) + if attrId in self.__dict__: + return self.__dict__[attrId] + else: + return self.__getattr__(attr) + + def __dir__(self): + return (dir(self.__class__) + self.__dict__.keys()) + + def get_frame_slot_value(self, slot): + """ + Retrieve the slot data for frame from Pathway Tools. + + Return + the self PFrame, modified with the new slot with data. + """ + # FrameObject is a dictionary of slot names and values. + [slotName, value] = self.pgdb.sendPgdbFnCall('get-frame-slot-value', self.frameid, Symbol(slot)) + if not slotName: + raise PythonCycError("Slot " + slot + " does not exist for frame " + self.frameid + " from organism (orgid) " +self.pgdb._orgid) + # Modify slot name to allow Python's syntax (e.g., '_' instead of '-'). + self.__dict__[convertLispIdtoPythonId(slotName)] = value + return self + + def get_frame_data(self): + """ + Retrieve the frame data from Pathway Tools, that is, all slots and their values + for this PFrame are retrieved and stored locally. For a class, the instances are + not retrieved by this method. Instead, use method get_class_data applied to a + PGDB object. + + Return + the self PFrame, modified with the new slots and data. + """ + # FrameObject is a dictionary of slot names and values. + frameObject = self.pgdb.sendPgdbFnCall('get-frame-object', self.frameid) + if not frameObject: + raise PythonCycError("Could not retrieve frame " + self.frameid + " from organism (orgid) " + self.pgdb._orgid) + else: + self._gotframe = True + # Modify slot names to allow Python's syntax (e.g., '_' instead of '-'). + for slot in frameObject: + self.__dict__[convertLispIdtoPythonId(slot)] = frameObject[slot] + return self + + def __setattr__(self, attr, val): + if not attr.startswith('_'): + raise PythonCycError("PFrames are read only objects. Attributes of PFrame objects cannot be modified " + str((self.frameid,attr,val)) + ". You can only modify slot frames for the PGDB in the running Pathway Tools by using methods put_slot_value or put_slot_values using a PGDB object.") + self.__dict__[attr] = val + return None + + def __setitem__(self, attr, val): + if not attr.startswith('_'): + raise PythonCycError("PFrames are read only objects. Attributes of PFrame objects cannot be modified " + str((self.frameid,attr,val)) + ". You can only modify slot frames for the PGDB in the running Pathway Tools by using methods put_slot_value or put_slot_values using a PGDB object.") + self.__dict__[attr] = val + return None + + def __str__(self): + if self._isclass: + return '' + else: + return '' + + def __repr__(self): + if self._isclass: + return self.__str__() + else: + return str(self.__dict__) + + if 'IPython' in sys.modules: + def _ipython_display_(self): + table = '' + if not self._isclass: + for attr in sorted(self.__dict__): + if not (attr.startswith('_')): + table = table + "" + str(attr) + "" + str(self.__dict__[attr]) + "" + else: + table = table + 'Class ' + self.frameid + ' has ' + str(self._nb_pframes()) + ' instances' + if table == '': + table = '' + self.__str__() + '' + table = ''+ table + '
' + display(HTML(table)) + + def _nb_pframes(self): + return len(self.instances) + + def __eq__(self, frame): + # If the given frame is a string, it is assumed to be a frameid. + if isinstance(frame, str): + return self.frameid == frame + # Otherwise it could be a Frame. + elif isinstance(frame, PFrame): + # TBD: should we consider the name of the pgdb? + return (self.pgdb == frame.pgdb) and (self.frameid == frame.frameid) + # Otherwise it cannot be equal to this object. + else: return False + + def __ne__(self, frame): + return not self.__eq__(frame) diff --git a/pythoncyc/__init__.py b/pythoncyc/__init__.py index 26d6057..ad40723 100644 --- a/pythoncyc/__init__.py +++ b/pythoncyc/__init__.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -56,9 +56,9 @@ def so(orgid): return select_organism(orgid) def all_orgids(): - """ - Returns all organism unique ids (orgids) available - from the current running Pathway Tools. + """ + Returns all organism unique ids (orgids) available + from the current running Pathway Tools. """ orgids = sendQueryToPTools('(all-orgids)') return orgids @@ -66,12 +66,12 @@ def all_orgids(): def biovelo(query): """ Execute a BioVelo query and return the result. - + Parameters query: a string, which is a BioVelo query. - Returns + Returns Whatever the BioVelo query computes. - + Example bv('[(p, reactions-of-pathway(p)): p<-ecoli^^pathways]') """ @@ -93,4 +93,3 @@ def run_fba(fileName): in file PGDB.py. """ return sendQueryToPTools('(python-run-fba "'+fileName+'")') - diff --git a/pythoncyc/config.py b/pythoncyc/config.py index 04c57d8..6bb72da 100644 --- a/pythoncyc/config.py +++ b/pythoncyc/config.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -21,10 +21,10 @@ # ---------------------------------------------------------------------- """ -This module can be used to set various parameters for PythonCyc, -in particular to set debug on or off, the host name and port number -of the running Pathway Tools' Python server. By default, the Pathway Tools -Python server is running locally on port 5008. +This module can be used to set various parameters for PythonCyc, in particular +to set debug on or off, the host name and port number of the running Pathway +Tools' Python server. By default, the Pathway Tools Python server is running +locally on port 5008. """ _debug = False @@ -32,30 +32,31 @@ _hostport = 5008 def set_debug_on(): - """ - Turn on debug mode for PythonCyc. - Turning on debugging should turn on output tracings of the communications between PythonCyc and Pathway Tools. - """ - global _debug - _debug = True - print 'Debug on.' - -def set_debug_off(): - """ - Turn off debug mode for PythonCyc. - Turning off debugging should turn off all output tracings of the communications between PythonCyc and Pathway Tools. + """ + Turn on debug mode for PythonCyc. + Turning on debugging should turn on output tracings of the communications + between PythonCyc and Pathway Tools. + """ + global _debug + _debug = True + print 'Debug on.' - """ - global _debug - _debug = False - print 'Debug off.' +def set_debug_off(): + """ + Turn off debug mode for PythonCyc. + Turning off debugging should turn off all output tracings of the communications + between PythonCyc and Pathway Tools. + """ + global _debug + _debug = False + print 'Debug off.' def set_host_name(hostname): - global _hostname - _hostname = hostname - print 'PythonCyc will communicate with Pathway Tools running on host name ',_hostname + global _hostname + _hostname = hostname + print 'PythonCyc will communicate with Pathway Tools running on host name ', _hostname def set_host_port(hostport): - global _hostport - _hostport = hostport - print 'PythonCyc will communicate with Pathway Tools running on host port ',_hostport + global _hostport + _hostport = hostport + print 'PythonCyc will communicate with Pathway Tools running on host port ', _hostport diff --git a/setup.py b/setup.py index ac4ad2f..34cb52d 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ # Copyright (c) 2014, SRI International -# +# # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including @@ -7,10 +7,10 @@ # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: -# +# # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND @@ -20,15 +20,23 @@ # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # ---------------------------------------------------------------------- -from distutils.core import setup +# removed distutils because pip cannot uninstall PythonCyc +#from distutils.core import setup +from setuptools import setup, find_packages -setup( - name='PythonCyc', - version='1.0', - author='Mario Latendresse', - author_email='latendre@ai.sri.com', - packages=['pythoncyc'], - license='LICENSE', - description='A Python interface to Pathway Tools', - long_description=open('README.md').read() - ) +def main(): + # include other folders in the python packages + + setup( + name='PythonCyc', + version='1.0', + author='Mario Latendresse', + author_email='latendre@ai.sri.com', + packages=['pythoncyc'], + license='LICENSE', + description='A Python interface to Pathway Tools', + long_description=open('README.md').read() + ) + +if __name__ == '__main__': + main() From 2b523c191ee24a8b157af59833e82fc75c188ca8 Mon Sep 17 00:00:00 2001 From: glucksfall Date: Fri, 15 Mar 2019 12:26:18 -0300 Subject: [PATCH 02/17] Added CHANGES.md --- CHANGES.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 CHANGES.md diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 0000000..d31c260 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,50 @@ +# pythoncyc-notebooks + +Section 5 API functions +- Section 5.1 enumeration functions +* The documentation of the function all-rxns has the argument type that could be set to non-spontaneous. However, the valid cases are :ALL, :PROTEIN-SMALL-MOLECULE-REACTION, :PROTEIN-REACTION, :TRNA-REACTION, :SPONTANEOUS, :SPONTANEOUS-HT, :ENZYME, :ENZYME-HT, :SMALL-MOLECULE, :SMALL-MOLECULE-HT, :METAB-PATHWAYS, :ALL-RXNS-METAB-PATHWAYS-WITH-DUPLICATES-HT, :METAB-SMM, :SMM, :METAB-SMM-HT, :METAB-COMPLETE-SMM, :METAB-ALL, :TRANSPORT-HT, :TRANSPORT, and :ENZYME-NOT-IN-PWY. The docstring was updated with the valid cases (but not their descriptions). +* The documentation of the function all_transported_chemicals has a valid argument show_compartment. However, the pythoncyc API doesn't include the argument. Added the keyword to PGDB.py, line 787. Tested in pathway tools lisp interpreter with (with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :show-compartment 'CCO-CYTOSOL )) returning a list of instances and classes, but I doubt if I give a valid show-compartment keyword. + +- Section 5.1.1 operations on reactions +* The documentation of the function enzymes_of_reaction has the arguments experimental-only? and local-only-p. However, the pythoncyc API has close similar experimental_only and local_only arguments. To be consistent with documentation, I changed the local_only argument to local_only_p. +* The documentation has the description for the rxn-without-sequenced-enzyme-p function, but the lisp function is reaction-without-sequenced-enzyme-p. Moreover, the describe function says reaction-without-sequenced-enzyme-p doesn't recognize the argument complete?. I tested in the lisp interpreter with (with-organism (:org-id '|ECOLI|) (reaction-without-sequenced-enzyme-p '|RXN-15348| )) returning T. However when I run the code in python, it fails with An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode. +* The function pathway-hole-p don't have the argument hole-if-any-gene-without-position? as tested with the describe function in the lisp interpreter. I deleted the argument from the API. +* The function rxn-present? is incorrectly queried as rxn-present-p. Tested with (with-organism (:org-id '|ECOLI|) (rxn-present? '|RXN-15348| )) returning T. Moreover, the lisp function has the INCLUDE-SPONTANEOUS? argument absent from the documentation and from the API: (with-organism (:org-id '|ECOLI|) (rxn-present? '|RXN-15348| :INCLUDE-SPONTANEOUS )) returns T, but fails if (with-organism (:org-id '|ECOLI|) (rxn-present? '|RXN-15348| :INCLUDE-SPONTANEOUS? T )). I don't know (yet) how to add the argument to the code. +* The documentation describes the function compartment-of-rxn but it isn't a function or wasn't defined as a function. Tested with (describe 'compartment-of-rxn). + +- Section 5.1.2 Operations on pathways +* sorted argument of functions genes_of_pathway and enzymes_of_pathway now works. Probably it should be renamed because of a clash with the python sorted function. + +- Section 5.1.3 Operations on Enzymatic Reactions +* er argument of functions enzrxn_activators and enzrxn_inhibitors was changed to enzrxn for consistency with other functions. +* function pathway-allows-enzrxn is implemented in ptools as pathway-allows-enzrxn?, but gives the following error: function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode + +- Section 5.1.4 Operations on Proteins. +* p argument of functions monomers_of_protein and base_components_of_protein changed to protein for consistency with other functions +* functions reduce_modified_proteins and genes_of_proteins always require a list of proteins, even if the list has only one element. I added a check to make sure the functions work even if the user mistakenly gives a single frameid. +* the argument INCLUDE-SUBREACTIONS? from function reactions-of-enzyme is undocumented. I included it in the pythoncyc API. I don't know how to use the kb argument of the function +* incomplete documentation for enzyme_p; argument type admits non-transport-non-pathway and the argument was renamed to type_of_reactions because of clash with python type function +* LEADER-PEPTIDE-P is implemented as LEADER-PEPTIDE?. Changes don't work similarly to pathway-allows-enzrxn?. +* argument compartments is mandatory but it wasn't present in function protein_in_compartment_p. Added to the function and works correctly. +* problem: (with-organism (:org-id '|ECOLI|) (all-transporters-across :membranes '|CCO-MEMBRANE| )) returns NIL when it should be equivalent to (with-organism (:org-id '|ECOLI|) (all-transporters-across :membranes :all )), according to the documentation + +- Section 5.1.5 Operations on Genes. +* item argument on function gene_p changed to gene for consistency with ther function +* INCLUDE-GENE-PROD-AS-SUBSTRATE? argument of function pathways-of-gene is undocumented and not present in pythoncyc API and it was added. As well, argument INCLUDE-SUPER-PWYS? is now correctly interpreted. +* documentation has the function connecting-genes but isn't present in ptools. Tested with (apropos "connecting") +* documentation states that argument max-gap of functions gene-clusters and neighboring-genes-p is optional, but the API set it to None. Changed to 10 to match the documentation. +* adjacent_genes_p and neighboring_genes_p functions check if the two genes are the same, returning None if they are "adjacent" or "neighbors" +* rna_coding_gene is implemented as rna_coding_gene?. Changed and tested with (with-organism (:org-id '|ECOLI|) (rna-coding-gene? '|EG11414| )) but pythoncyc fails similarly to pathway-allows-enzrxn? + +- Section 5.1.6 Operations on Regulatory Frames +* transcription_factor_p is implemented as transcription-factor? and regulator_of_type as regulator_of_type?. Both work correctly in the lisp interpreter but pythoncyc fails similarly as pathway-allows-enzrxn? +* regulators_of_operon_transcription function accept only lists, similarly to reduce_modified_proteins, also modified in the same way to ensure the function receives a list even if the user gives a single frameid. +* problem: I don't know how to use the mode argument in transcription_factor_ligands function, therefore I don't know if the function works or not. + +- Section 5.1.7 Operations on Compounds +* substrate-of-generic-rxn is implemented as substrate-of-generic-rxn?, works in the interpreter but not from pythoncyc. +* documentation defines the function activated-or-inhibited-by-compound, but pythoncyc has the deactivated-or-inhibited-by-compound. I modified the function but raises the error function is not allowed to be called in restricted mode, but works in the lisp interpreter. I'm out of ideas for the reason of this recurrent error. + +- Section 5.1.8 Object Name Manipulation Operations +* get-name-string fails and working on it +* full_enzyme_name optional arguments were included in the function, been the reason of failure. Changed to kwargs and working From ca8673c94aea996f286a91811db64351a85060b5 Mon Sep 17 00:00:00 2001 From: glucksfall Date: Fri, 15 Mar 2019 12:29:27 -0300 Subject: [PATCH 03/17] Added CHANGES.md --- CHANGES.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index d31c260..57669a5 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,4 +1,9 @@ -# pythoncyc-notebooks +# CHANGES proposed to PythonCyc 1.0 +# Rodrigo Santibáñez @ Network Biology Lab (NBL), Universidad Mayor, 2019 + +# Beware that there is a number of functions that works in the +# pathway tools lisp interpreter (ptlisp), but no from the python interface. +# For those functions, the API prints the query to the standard output. Section 5 API functions - Section 5.1 enumeration functions From 20c5f30795318842613d94077817ccd3258c78fa Mon Sep 17 00:00:00 2001 From: glucksfall Date: Tue, 9 Apr 2019 14:45:49 -0400 Subject: [PATCH 04/17] print statements compatible with Py3 --- pythoncyc/PGDB.py | 26 ++++++++++++++++---------- pythoncyc/PTools.py | 12 ++++++------ pythoncyc/__init__.py | 4 ++-- pythoncyc/config.py | 8 ++++---- setup.py | 8 ++++---- 5 files changed, 32 insertions(+), 26 deletions(-) diff --git a/pythoncyc/PGDB.py b/pythoncyc/PGDB.py index 356eed2..a9a6e5b 100644 --- a/pythoncyc/PGDB.py +++ b/pythoncyc/PGDB.py @@ -155,7 +155,8 @@ def prepareFnCall(fn, *args, **kwargs): for key in kwargs if kwargs[key] != None ]) lisp_query = '(' + fn + ' ' + args2 + ' ' + keywords + ')' - print lisp_query + if config._debug: + print(lisp_query) return lisp_query class PGDB(): @@ -172,7 +173,7 @@ def __init__(self, orgid): Python, such as ecoli.reactions. """ if config._debug: - print "PGDB __init__" + print("PGDB __init__") self._orgid = "unknown" self._error = False @@ -238,7 +239,10 @@ def __getattr__(self, attr): automatically when the corresponding instances or classes exist in the PGDB. """ if config._debug: - print "PGDB ", self._orgid, "__getattr__", attr + print("PGDB ") + print(self._orgid) + print("__getattr__") + print(attr) # If the converted attribute exists as an attribute. attrId = convertLispIdtoPythonId(attr) @@ -269,7 +273,7 @@ def __getattr__(self, attr): def _ipython_display_(self): table = "" # A PGDB frame may contain thousands of attributes, one - # for each instance. This output is too large to print in + # for each instance. This output is too large to printin # most cases. Print a succinct representation of the PGDB frame. table = table + "" table = table + "" @@ -286,7 +290,7 @@ def __setitem__(self, attr, val): def __getitem__(self, index): if config._debug: - print "PGDB __getitem__", index + print"PGDB __getitem__", index if (isinstance(index,int) or isinstance(index,slice)) : if self._frames: return self._frames[index] @@ -351,11 +355,12 @@ def sendPgdbQuery(self, query): """ # Evaluate a query in the context of this PGDB. if self._orgid == "unknown": - print "Cannot send any query because the selected organism is unknown." + print("Cannot send any query because the selected organism is unknown.") return None else: lisp_query = '(with-organism (:org-id \'' + self._orgid + ') ' + query + ')' - print lisp_query + if config._debug: + print(lisp_query) return PTools.sendQueryToPTools(lisp_query) def sendPgdbFnCall(self, fn, *args, **kwargs): @@ -364,7 +369,8 @@ def sendPgdbFnCall(self, fn, *args, **kwargs): kwargs (keyword args) and return the result. If multiple values are returned by fn, the Pathway Tools Python server transforms them into a list. """ - print fn + if config._debug: + print(fn) fnCall = prepareFnCall(fn, *args, **kwargs) return self.sendPgdbQuery(fnCall) @@ -2373,7 +2379,7 @@ def adjacent_genes_p(self, g1, g2): A list if genes are in the same replicon. Otherwise False. """ if g1 == g2: - print "genes are the same." + print("both queries are the same.") return None else: return self.sendPgdbFnCallBool('adjacent-genes?', may_be_frameid(g1), may_be_frameid(g2)) @@ -2397,7 +2403,7 @@ def neighboring_genes_p(self, g1, g2, max_gap=10): A boolean value. """ if g1 == g2: - print "genes are the same." + print("both queries are the same.") return None else: return self.sendPgdbFnCallBool('neighboring-genes-p', may_be_frameid(g1), may_be_frameid(g2), max_gap) diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index 386d73a..1d5c8ae 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -51,7 +51,7 @@ def recvAll(s): the message received on socket s as a string. """ if config._debug: - print 'recvAll ...' + print('recvAll ...') # Get the type of message which is one character long. type = s.recv(1) @@ -64,7 +64,7 @@ def recvAll(s): # The next 10 characters give the length. lengthMsg = int(recvFixedLength(s, 10)) if config._debug: - print "lengthMsg ", lengthMsg + print("lengthMsg {:d}".format(lengthMsg)) return recvFixedLength(s, lengthMsg) else: # Something is broken on the server side, so @@ -164,10 +164,10 @@ def sendQueryToPTools(query): query, a string that the Python server in Pathway Tools can evaluate. Returns - The result of the query, as a Python object, decoded by Json. + The result of the query, as a Python object, decoded by JSON. """ if config._debug: - print 'Sending query ' + query + print('Sending query ' + query) if config._hostname == '': raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') @@ -185,11 +185,11 @@ def sendQueryToPTools(query): sendAll(s, query) if config._debug: - print 'Sent ' + query + ' to Pathway Tools.' + print('Sent ' + query + ' to Pathway Tools.') response = recvAll(s) if config._debug and len(response) < 4000: - print 'JSON Received: ', response + print('JSON Received: {:s}'.format(response)) r = json.loads(response) s.close() diff --git a/pythoncyc/__init__.py b/pythoncyc/__init__.py index ad40723..2fa979b 100644 --- a/pythoncyc/__init__.py +++ b/pythoncyc/__init__.py @@ -75,7 +75,7 @@ def biovelo(query): Example bv('[(p, reactions-of-pathway(p)): p<-ecoli^^pathways]') """ - return sendQueryToPTools('(biovelo "'+query+'")') + return sendQueryToPTools('(biovelo "' + query + '")') def bv(query): """ @@ -92,4 +92,4 @@ def run_fba(fileName): For the documentation of this function, see method run_fba in file PGDB.py. """ - return sendQueryToPTools('(python-run-fba "'+fileName+'")') + return sendQueryToPTools('(python-run-fba "' + fileName + '")') diff --git a/pythoncyc/config.py b/pythoncyc/config.py index 6bb72da..cfa28e8 100644 --- a/pythoncyc/config.py +++ b/pythoncyc/config.py @@ -39,7 +39,7 @@ def set_debug_on(): """ global _debug _debug = True - print 'Debug on.' + print('Debug on.') def set_debug_off(): """ @@ -49,14 +49,14 @@ def set_debug_off(): """ global _debug _debug = False - print 'Debug off.' + print('Debug off.') def set_host_name(hostname): global _hostname _hostname = hostname - print 'PythonCyc will communicate with Pathway Tools running on host name ', _hostname + print('PythonCyc will communicate with Pathway Tools running on host name {:s}'.format(_hostname)) def set_host_port(hostport): global _hostport _hostport = hostport - print 'PythonCyc will communicate with Pathway Tools running on host port ', _hostport + print('PythonCyc will communicate with Pathway Tools running on host port {:d}'.format(_hostport)) diff --git a/setup.py b/setup.py index 34cb52d..45f8992 100644 --- a/setup.py +++ b/setup.py @@ -29,12 +29,12 @@ def main(): setup( name='PythonCyc', - version='1.0', - author='Mario Latendresse', - author_email='latendre@ai.sri.com', + version='2.0', + author='Rodrigo Santibáñez', + author_email='glucksfall@users.noreply.github.com', packages=['pythoncyc'], license='LICENSE', - description='A Python interface to Pathway Tools', + description='A Python interface to Pathway Tools, 2019 update', long_description=open('README.md').read() ) From f597714a5495db1d4350a3443599127aca33baa2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Wed, 10 Apr 2019 19:23:56 -0400 Subject: [PATCH 05/17] Py3 compatibility --- pythoncyc/PGDB.py | 14 ++++---- pythoncyc/PTools.py | 76 ++++++++++++++++++++-------------------- pythoncyc/PToolsFrame.py | 10 +++--- pythoncyc/__init__.py | 6 ++-- 4 files changed, 53 insertions(+), 53 deletions(-) diff --git a/pythoncyc/PGDB.py b/pythoncyc/PGDB.py index a9a6e5b..1c6c567 100644 --- a/pythoncyc/PGDB.py +++ b/pythoncyc/PGDB.py @@ -20,11 +20,11 @@ # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # ---------------------------------------------------------------------- -import PTools import sys -import config -from PTools import PToolsError, PythonCycError -from PToolsFrame import Symbol, PFrame, convertLispIdtoPythonId +import pythoncyc.PTools +import pythoncyc.config +from pythoncyc.PTools import PToolsError, PythonCycError +from pythoncyc.PToolsFrame import Symbol, PFrame, convertLispIdtoPythonId if 'IPython' in sys.modules: from IPython.display import display, HTML @@ -183,7 +183,7 @@ def __init__(self, orgid): # Verify that the running Pathway Tools has the PGDB (organism). try: r = PTools.sendQueryToPTools('(orgid-exist-p \'' + orgid + ')') - except PToolsError, msg: + except PToolsError as msg: raise PythonCycError('Pathway Tools was unable to verify if organism (orgid) {:s} is known in your running Pathway Tools. More specifically: {:s}'.format(orgid, msg)) if not r: raise PythonCycError("The organism orgid {:s} is unknown. Use pythoncyc.all_orgids() to get a list of known orgids.".format(orgid)) @@ -270,7 +270,7 @@ def __getattr__(self, attr): return None if 'IPython' in sys.modules: - def _ipython_display_(self): + def _ipython_display_(self): table = "
orgid" + self._orgid + "
Number of PFrames" + str(self._nb_pframes()) + "
" # A PGDB frame may contain thousands of attributes, one # for each instance. This output is too large to printin @@ -290,7 +290,7 @@ def __setitem__(self, attr, val): def __getitem__(self, index): if config._debug: - print"PGDB __getitem__", index + print("PGDB __getitem__", index) if (isinstance(index,int) or isinstance(index,slice)) : if self._frames: return self._frames[index] diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index 1d5c8ae..a6c2603 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -26,14 +26,10 @@ only toplevel functions and some simple classes for errors handling. """ -import os -import sys -import socket as so -import json -import time -import config - -def recvAll(s): +import json, os, sys, socket, time +import pythoncyc.config + +def recvAll(msg): """ Description Receive the entire message sent by Pathway Tools on socket s. The message starts @@ -50,33 +46,34 @@ def recvAll(s): Return the message received on socket s as a string. """ - if config._debug: + if pythoncyc.config._debug: print('recvAll ...') # Get the type of message which is one character long. - type = s.recv(1) + msg_type = msg.recv(1) - # print "type ", type - if type == 'A': + if pythoncyc.config._debug: + print("type ", msg_type) + if msg_type == 'A': # The length of the message is not given, use time out approach. - return recvTimeOut(s) - elif type == 'L': + return recvTimeOut(msg) + elif msg_type == 'L': # The next 10 characters give the length. - lengthMsg = int(recvFixedLength(s, 10)) + lengthMsg = int(recvFixedLength(msg, 10)) if config._debug: print("lengthMsg {:d}".format(lengthMsg)) - return recvFixedLength(s, lengthMsg) + return recvFixedLength(msg, lengthMsg) else: # Something is broken on the server side, so # use recv with a long timeout to try flushing # the sent message. - return recvTimeOut(s, timeOut=5) + return recvTimeOut(msg, timeOut=5) -def sendAll(s, query): +def sendAll(so, query): sent_len = 0 query_len = len(query) while sent_len < query_len: - nb_chars = s.send(query[sent_len:]) + nb_chars = so.send(query[sent_len:]) if nb_chars == 0: raise PythonCycError("Connection to Pathway Tools broke while sending query {:s}.".format(query)) sent_len = sent_len + nb_chars @@ -104,7 +101,7 @@ def recvFixedLength(s, lengthMsg): # print 'Fixed receive: ', ''.join(pieces) return ''.join(pieces) -def recvTimeOut(socket, timeOut=2): +def recvTimeOut(open_socket, timeOut=2): """ Description Receive a message of unknown length on socket. While receiving a message, if no @@ -114,7 +111,7 @@ def recvTimeOut(socket, timeOut=2): is received after 60 seconds, this method returns with an empty message. Parms - socket + open_socket an open network socket. timeOut number of seconds before timing out between fragments of the received message. @@ -137,15 +134,16 @@ def recvTimeOut(socket, timeOut=2): break # Try to receive some text. try: - data = socket.recv(4096) + data = open_socket.recv(4096) if data: - pieces.append(data) + print(data) + pieces.append(data.decode()) # Reset beginning time for next recv. begin = time.time() else: # Slow down in case timeOut is small. time.sleep(0.1) - except so.error: + except open_socket.error: pass # Join all the pieces together. @@ -166,32 +164,34 @@ def sendQueryToPTools(query): Returns The result of the query, as a Python object, decoded by JSON. """ - if config._debug: + if pythoncyc.config._debug: print('Sending query ' + query) - if config._hostname == '': + if pythoncyc.config._hostname == '': raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') try: - s = so.socket(so.AF_INET, so.SOCK_STREAM) + open_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) # Make socket non blocking. - s.setblocking(0) - s.settimeout(360) # The query may take a long time in some cases. - s.connect((config._hostname, config._hostport)) - except so.error, msg: - raise PToolsError('Failed to create a connection to a running Pathway Tools at ' + config._hostname + ' on port ' + str(config._hostport) + '. Make sure Pathway Tools is running with option -python. Error code: ' + str(msg[0]) + ', error message: ' + msg[1]) + open_socket.setblocking(0) + open_socket.settimeout(360) # The query may take a long time in some cases. + open_socket.connect((pythoncyc.config._hostname, pythoncyc.config._hostport)) + + except socket.error as msg: + raise PToolsError('Failed to create a connection to a running Pathway Tools at ' + pythoncyc.config._hostname + ' on port ' + str(pythoncyc.config._hostport) + '. Make sure Pathway Tools is running with option -python. Error code: ' + str(msg[0]) + ', error message: ' + msg[1]) # Send, receive and close socket. - sendAll(s, query) + sendAll(open_socket, query.encode()) - if config._debug: + if pythoncyc.config._debug: print('Sent ' + query + ' to Pathway Tools.') - response = recvAll(s) - if config._debug and len(response) < 4000: - print('JSON Received: {:s}'.format(response)) + response = recvAll(open_socket) + print(response) + #if pythoncyc.config._debug and len(response) < 4000: + print('JSON Received: {:s}'.format(response)) r = json.loads(response) - s.close() + open_socket.close() if isinstance(r, basestring) and r.startswith(':error'): raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(r)) diff --git a/pythoncyc/PToolsFrame.py b/pythoncyc/PToolsFrame.py index 4d209b4..561daf6 100644 --- a/pythoncyc/PToolsFrame.py +++ b/pythoncyc/PToolsFrame.py @@ -26,8 +26,8 @@ """ import sys -import config -from PTools import PToolsError, PythonCycError +import pythoncyc.config +from pythoncyc.PTools import PToolsError, PythonCycError if 'IPython' in sys.modules: from IPython.display import display, HTML @@ -117,13 +117,13 @@ def vectorize_dict(self): def __getslice__(self, i, j, stride = None): if config._debug: - print 'PFrame __getslice__ ', i, j, stride + print('PFrame __getslice__ ', i, j, stride) return self.instances[i:j:stride] def __getattr__(self, attr): # Accessing a slot of the frame using attribute syntax (e.g. r.left) if config._debug: - print 'PFrame __getattr__ ', attr + print('PFrame __getattr__ ', attr) if attr in self.__dict__: return self.__dict__[attr] @@ -146,7 +146,7 @@ def __getattr__(self, attr): def __getitem__(self,attr): if config._debug: - print "PFrame __getitem__ ", attr + print("PFrame __getitem__ ", attr) # The slice case is for attr = slice(i,j,s) if (isinstance(attr,int) or isinstance(attr, slice)): if 'instances' in self.__dict__: diff --git a/pythoncyc/__init__.py b/pythoncyc/__init__.py index 2fa979b..15115dc 100644 --- a/pythoncyc/__init__.py +++ b/pythoncyc/__init__.py @@ -40,9 +40,9 @@ Please consult the tutorial.html file, under directory doc, for more information about how to use PythonCyc. """ - -from PGDB import PGDB -from PTools import sendQueryToPTools +import pythoncyc.config +from pythoncyc.PGDB import PGDB +from pythoncyc.PTools import sendQueryToPTools def select_organism(orgid): """ From b5b3744195cccfc71b4bd552b95ac74d4a7f1ea8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Thu, 11 Apr 2019 01:48:12 -0400 Subject: [PATCH 06/17] Python3 only --- pythoncyc/PTools.py | 48 ++++++++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index a6c2603..f74cd5d 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -29,10 +29,10 @@ import json, os, sys, socket, time import pythoncyc.config -def recvAll(msg): +def recvAll(open_socket): """ Description - Receive the entire message sent by Pathway Tools on socket s. The message starts + Receive the entire message sent by Pathway Tools on an open socket. The message starts with a single character type, which is either 'A' or 'L'. The 'A' time is used without providing a length but can take longer to receive because it uses a timeout technique to read the entire message. The 'L' type assumes that the @@ -41,7 +41,7 @@ def recvAll(msg): characters. Parm - s, an open network socket. + open_socket, an open network socket. Return the message received on socket s as a string. @@ -50,38 +50,39 @@ def recvAll(msg): print('recvAll ...') # Get the type of message which is one character long. - msg_type = msg.recv(1) + msg_type = open_socket.recv(1) if pythoncyc.config._debug: print("type ", msg_type) - if msg_type == 'A': + + if msg_type == b'A': # The length of the message is not given, use time out approach. - return recvTimeOut(msg) - elif msg_type == 'L': + return recvTimeOut(open_socket) + elif msg_type == b'L': # The next 10 characters give the length. - lengthMsg = int(recvFixedLength(msg, 10)) - if config._debug: + lengthMsg = int(recvFixedLength(open_socket, 10)) + if pythoncyc.config._debug: print("lengthMsg {:d}".format(lengthMsg)) - return recvFixedLength(msg, lengthMsg) + return recvFixedLength(open_socket, lengthMsg) else: # Something is broken on the server side, so # use recv with a long timeout to try flushing # the sent message. - return recvTimeOut(msg, timeOut=5) + return recvTimeOut(open_socket, timeOut=5) -def sendAll(so, query): +def sendAll(open_socket, query): sent_len = 0 query_len = len(query) while sent_len < query_len: - nb_chars = so.send(query[sent_len:]) + nb_chars = open_socket.send(query[sent_len:]) if nb_chars == 0: raise PythonCycError("Connection to Pathway Tools broke while sending query {:s}.".format(query)) sent_len = sent_len + nb_chars -def recvFixedLength(s, lengthMsg): +def recvFixedLength(open_socket, lengthMsg): """ Description - Receive a fixed length message on socket s. + Receive a fixed length message on an open socket. Parm lengthMsg, an integer, which is the length in characters of the message to receive. @@ -92,11 +93,11 @@ def recvFixedLength(s, lengthMsg): pieces = [] nbBytesRecv = 0 while nbBytesRecv < lengthMsg: - piece = s.recv(min(lengthMsg - nbBytesRecv, 4096)) + piece = open_socket.recv(min(lengthMsg - nbBytesRecv, 4096)) if piece == '': # Give up now because nothing was received. return ''.join(pieces) - pieces.append(piece) + pieces.append(piece.decode()) nbBytesRecv = nbBytesRecv + len(piece) # print 'Fixed receive: ', ''.join(pieces) return ''.join(pieces) @@ -143,7 +144,7 @@ def recvTimeOut(open_socket, timeOut=2): else: # Slow down in case timeOut is small. time.sleep(0.1) - except open_socket.error: + except socket.error: pass # Join all the pieces together. @@ -187,17 +188,16 @@ def sendQueryToPTools(query): print('Sent ' + query + ' to Pathway Tools.') response = recvAll(open_socket) - print(response) - #if pythoncyc.config._debug and len(response) < 4000: - print('JSON Received: {:s}'.format(response)) - r = json.loads(response) + if pythoncyc.config._debug and len(response) < 4000: + print('JSON Received: {:s}'.format(response)) + msg = json.loads(response) open_socket.close() - if isinstance(r, basestring) and r.startswith(':error'): + if isinstance(msg, str) and r.startswith(':error'): raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(r)) else: # Return some result. - return r + return msg class PythonCycError(Exception): """ From d707202cc139e7b281f8030bd775af5db923c0d7 Mon Sep 17 00:00:00 2001 From: glucksfall Date: Thu, 11 Apr 2019 02:09:06 -0400 Subject: [PATCH 07/17] some other Py2 to Py3 changes --- pythoncyc/PGDB.py | 31 ++++++++++++++----------------- pythoncyc/PTools.py | 4 ++-- pythoncyc/PToolsFrame.py | 6 +++--- 3 files changed, 19 insertions(+), 22 deletions(-) diff --git a/pythoncyc/PGDB.py b/pythoncyc/PGDB.py index 1c6c567..c55b224 100644 --- a/pythoncyc/PGDB.py +++ b/pythoncyc/PGDB.py @@ -21,8 +21,8 @@ # ---------------------------------------------------------------------- import sys -import pythoncyc.PTools import pythoncyc.config +import pythoncyc.PTools as PTools from pythoncyc.PTools import PToolsError, PythonCycError from pythoncyc.PToolsFrame import Symbol, PFrame, convertLispIdtoPythonId @@ -51,7 +51,7 @@ def may_be_frameid(obj): return [ may_be_frameid(y) for y in obj ] elif isinstance(obj, PFrame): return obj - elif isinstance(obj, basestring): + elif isinstance(obj, str): return Symbol(obj) else: raise PythonCycError('Error: the argument must a string or a PFrame, but given {0}.'.format(x)) @@ -66,7 +66,7 @@ def mkey(obj): Returns if obj is a string, it is suffixed by ':', otherwise obj itself. """ - if isinstance(obj, basestring): + if isinstance(obj, str): return ':' + obj else: return obj @@ -89,7 +89,7 @@ def convertArgToLisp(arg, inquote=False): return ("" if inquote else "'") + arg._name # Type basestring includes string and unicode string. - elif isinstance(arg, basestring): + elif isinstance(arg, str): # It is either a symbol, a string or a keyword. # If it starts and ends with '|', assumes it is a symbol and add # a quote if not already in a quoted context otherwise just @@ -110,7 +110,7 @@ def convertArgToLisp(arg, inquote=False): return 't' if arg else 'nil' elif arg == None: return 'nil' - elif isinstance(arg, (int, long, float, complex)): + elif isinstance(arg, (int, float, complex)): return str(arg) elif isinstance(arg, PFrame): # Just using the frameid is enough (there is no need to @@ -155,7 +155,7 @@ def prepareFnCall(fn, *args, **kwargs): for key in kwargs if kwargs[key] != None ]) lisp_query = '(' + fn + ' ' + args2 + ' ' + keywords + ')' - if config._debug: + if pythoncyc.config._debug: print(lisp_query) return lisp_query @@ -172,7 +172,7 @@ def __init__(self, orgid): many classes of objects can be retrieved by using the attribute syntax of Python, such as ecoli.reactions. """ - if config._debug: + if pythoncyc.config._debug: print("PGDB __init__") self._orgid = "unknown" self._error = False @@ -238,11 +238,8 @@ def __getattr__(self, attr): may exist as an instance or as a class. PFrame instances and classes are created automatically when the corresponding instances or classes exist in the PGDB. """ - if config._debug: - print("PGDB ") - print(self._orgid) - print("__getattr__") - print(attr) + if pythoncyc.config._debug: + print("PGDB ", self._orgid, "__getattr__", attr) # If the converted attribute exists as an attribute. attrId = convertLispIdtoPythonId(attr) @@ -289,7 +286,7 @@ def __setitem__(self, attr, val): return None def __getitem__(self, index): - if config._debug: + if pythoncyc.config._debug: print("PGDB __getitem__", index) if (isinstance(index,int) or isinstance(index,slice)) : if self._frames: @@ -359,7 +356,7 @@ def sendPgdbQuery(self, query): return None else: lisp_query = '(with-organism (:org-id \'' + self._orgid + ') ' + query + ')' - if config._debug: + if pythoncyc.config._debug: print(lisp_query) return PTools.sendQueryToPTools(lisp_query) @@ -369,7 +366,7 @@ def sendPgdbFnCall(self, fn, *args, **kwargs): kwargs (keyword args) and return the result. If multiple values are returned by fn, the Pathway Tools Python server transforms them into a list. """ - if config._debug: + if pythoncyc.config._debug: print(fn) fnCall = prepareFnCall(fn, *args, **kwargs) return self.sendPgdbQuery(fnCall) @@ -482,7 +479,7 @@ def get_frame_objects(self, frameids): """ frameObjects = self.sendPgdbFnCallList('get-frame-objects', may_be_frameid(frameids)) pframes = [] - for frameid, slotsData in frameObjects.iteritems(): + for frameid, slotsData in frameObjects.items(): attrID = convertLispIdtoPythonId(frameid) if attrID in self.__dict__: f = self.__dict__[attrID] @@ -491,7 +488,7 @@ def get_frame_objects(self, frameids): self.__dict__[attrID] = f pframes.append(f) f._gotframe = True - for slot, data in slotsData.iteritems(): + for slot, data in slotsData.items(): f.__dict__[convertLispIdtoPythonId(slot)] = data return pframes diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index f74cd5d..2b1cb56 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -169,7 +169,7 @@ def sendQueryToPTools(query): print('Sending query ' + query) if pythoncyc.config._hostname == '': - raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') + raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function pythoncyc.config.set_hostname() to set the host name of your running Pathway Tools.') try: open_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) @@ -193,7 +193,7 @@ def sendQueryToPTools(query): msg = json.loads(response) open_socket.close() - if isinstance(msg, str) and r.startswith(':error'): + if isinstance(msg, str) and msg.startswith(':error'): raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(r)) else: # Return some result. diff --git a/pythoncyc/PToolsFrame.py b/pythoncyc/PToolsFrame.py index 561daf6..4d935af 100644 --- a/pythoncyc/PToolsFrame.py +++ b/pythoncyc/PToolsFrame.py @@ -116,13 +116,13 @@ def vectorize_dict(self): # End of definitions for pickle. def __getslice__(self, i, j, stride = None): - if config._debug: + if pythoncyc.config._debug: print('PFrame __getslice__ ', i, j, stride) return self.instances[i:j:stride] def __getattr__(self, attr): # Accessing a slot of the frame using attribute syntax (e.g. r.left) - if config._debug: + if pythoncyc.config._debug: print('PFrame __getattr__ ', attr) if attr in self.__dict__: @@ -145,7 +145,7 @@ def __getattr__(self, attr): return self.__dict__[attrId] def __getitem__(self,attr): - if config._debug: + if pythoncyc.config._debug: print("PFrame __getitem__ ", attr) # The slice case is for attr = slice(i,j,s) if (isinstance(attr,int) or isinstance(attr, slice)): From 1beef3750bb5b9ea05b72fd4dec8880cec69ad03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Sun, 14 Apr 2019 00:42:18 -0400 Subject: [PATCH 08/17] update examples --- .../ptools API - enumeration operations.ipynb | 607 +++--------------- pythoncyc/PGDB.py | 2 +- 2 files changed, 77 insertions(+), 532 deletions(-) diff --git a/examples/ptools API - enumeration operations.ipynb b/examples/ptools API - enumeration operations.ipynb index baf7523..7968ef8 100644 --- a/examples/ptools API - enumeration operations.ipynb +++ b/examples/ptools API - enumeration operations.ipynb @@ -4,25 +4,18 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "#to run the script, you need to start pathway tools form the command line \n", "# using the -lisp -python options. Example (from the pathway tools github repository)\n", "import os\n", "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" ] }, { @@ -33,7 +26,18 @@ { "data": { "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + "['',\n", + " '/usr/lib/python2.7',\n", + " '/usr/lib/python2.7/plat-x86_64-linux-gnu',\n", + " '/usr/lib/python2.7/lib-tk',\n", + " '/usr/lib/python2.7/lib-old',\n", + " '/usr/lib/python2.7/lib-dynload',\n", + " '/usr/local/lib/python2.7/dist-packages',\n", + " '/usr/lib/python2.7/dist-packages',\n", + " '/usr/lib/python2.7/dist-packages/gtk-2.0',\n", + " '/usr/local/lib/python2.7/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/shared/D1/opt/github-repositories/PythonCyc.networkbiolab']" ] }, "execution_count": 2, @@ -45,8 +49,12 @@ "# modify sys.path to recognize local pythoncyc\n", "import os\n", "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", "\n", "sys.path" ] @@ -65,9 +73,6 @@ } ], "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", "import pythoncyc\n", "all_orgids = pythoncyc.all_orgids()\n", "print all_orgids\n", @@ -81,18 +86,6 @@ "execution_count": 4, "metadata": {}, "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "all-pathways\n", - "(all-pathways ::small-molecule t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::small-molecule t ))\n" - ] - }, { "data": { "text/plain": [ @@ -124,8 +117,8 @@ "Otherwise, all pathways, including superpathways, will be returned. \n", "\"\"\"\n", "\n", - "ecoli.all_pathways(selector = u':all', base = True)[0:10]\n", - "ecoli.all_pathways(selector = u':small-molecule', base = True)[0:10]" + "ecoli.all_pathways(selector = 'all', base = True)[0:10]\n", + "ecoli.all_pathways(selector = 'small-molecule', base = True)[0:10]" ] }, { @@ -133,42 +126,6 @@ "execution_count": 5, "metadata": {}, "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "all-rxns\n", - "(all-rxns ::metab-pathways )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-pathways ))\n", - "all-rxns\n", - "(all-rxns ::metab-smm )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-smm ))\n", - "all-rxns\n", - "(all-rxns ::metab-all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::metab-all ))\n", - "all-rxns\n", - "(all-rxns ::transport )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::transport ))\n", - "all-rxns\n", - "(all-rxns ::small-molecule )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::small-molecule ))\n", - "all-rxns\n", - "(all-rxns ::protein-small-molecule-reaction )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::protein-small-molecule-reaction ))\n", - "all-rxns\n", - "(all-rxns ::protein-reaction )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::protein-reaction ))\n", - "all-rxns\n", - "(all-rxns ::trna-reaction )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::trna-reaction ))\n", - "all-rxns\n", - "(all-rxns ::spontaneous )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::spontaneous ))\n" - ] - }, { "data": { "text/plain": [ @@ -229,46 +186,42 @@ ":enzyme. \n", "\"\"\"\n", "\n", - "ecoli.all_rxns(type = ':all')[0:10]\n", - "ecoli.all_rxns(type = ':metab-pathways')[0:10]\n", - "ecoli.all_rxns(type = ':metab-smm')[0:10]\n", - "ecoli.all_rxns(type = ':metab-all')[0:10]\n", - "ecoli.all_rxns(type = ':transport')[0:10]\n", - "ecoli.all_rxns(type = ':small-molecule')[0:10]\n", - "ecoli.all_rxns(type = ':protein-small-molecule-reaction')[0:10]\n", - "ecoli.all_rxns(type = ':protein-reaction')[0:10]\n", - "ecoli.all_rxns(type = ':trna-reaction')[0:10]\n", - "ecoli.all_rxns(type = ':spontaneous')[0:10]" + "ecoli.all_rxns(type_of_reactions = 'all')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-pathways')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-smm')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-all')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'transport')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'small-molecule')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'protein-small-molecule-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'protein-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'trna-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:10]" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "all-rxns\n", - "(all-rxns ::spontaneous )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::spontaneous ))\n", - "all-substrates\n", - "(all-substrates '(|RXN-17635|) )\n", - "(with-organism (:org-id '|ECOLI|) (all-substrates '(|RXN-17635|) ))\n" + "[u'|RXN-17635|']\n" ] }, { - "data": { - "text/plain": [ - "[u'|Protein-Arginine-Aminocarbinol|',\n", - " u'|PROTON|',\n", - " u'|Protein-Arginine-Imidazolidine|']" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" + "ename": "PythonCycError", + "evalue": "Error: the argument must a string or a PFrame, but given |RXN-17635|.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mPythonCycError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 4\u001b[0m \"\"\"\n\u001b[1;32m 5\u001b[0m \u001b[0;32mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'spontaneous'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_substrates\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'|RXN-17635|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;31m#rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1][0])\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;32m/shared/D1/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.pyc\u001b[0m in \u001b[0;36mall_substrates\u001b[0;34m(self, rxns)\u001b[0m\n\u001b[1;32m 754\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mleft\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mright\u001b[0m \u001b[0mslots\u001b[0m \u001b[0mof\u001b[0m \u001b[0ma\u001b[0m \u001b[0mreaction\u001b[0m \u001b[0mframe\u001b[0m \u001b[0mcan\u001b[0m \u001b[0mcontain\u001b[0m \u001b[0mstrings\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 755\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 756\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallList\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'all-substrates'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 757\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 758\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mall_cofactors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.pyc\u001b[0m in \u001b[0;36mmay_be_frameid\u001b[0;34m(obj)\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mSymbol\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 56\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 57\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPythonCycError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Error: the argument must a string or a PFrame, but given {0}.'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 58\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 59\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mmkey\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPythonCycError\u001b[0m: Error: the argument must a string or a PFrame, but given |RXN-17635|." + ] } ], "source": [ @@ -276,132 +229,33 @@ "rxns\n", "A list of reaction frames. \n", "\"\"\"\n", - "\n", - "ecoli.all_substrates(rxns = ecoli.all_rxns(type = ':spontaneous')[0:1])" + "print(ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])\n", + "ecoli.all_substrates(u'|RXN-17635|')#rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1][0])" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-cofactors\n", - "(all-cofactors )\n", - "(with-organism (:org-id '|ECOLI|) (all-cofactors ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|DIPYRROMETHANE|',\n", - " u'|GTP|',\n", - " u'|UBIQUINONE-8|',\n", - " u'|AMMONIUM|',\n", - " u'|LYS|',\n", - " u'|HEME_O|',\n", - " u'|CPD-18260|',\n", - " u'|PQQ|',\n", - " u'|SIROHEME|',\n", - " u'|Mo-molybdopterin-cofactor|']" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ecoli.all_cofactors()[0:10]" ] }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-modulators\n", - "(all-modulators )\n", - "(with-organism (:org-id '|ECOLI|) (all-modulators ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|DEOXY-RIBOSE-1P|',\n", - " u'|CPD0-1546|',\n", - " u'|CPD0-1545|',\n", - " u'|NACL|',\n", - " u'|Gramicidins|',\n", - " u'|CPD0-1633|',\n", - " u'|G7642-MONOMER|',\n", - " u'|CPD-9229|',\n", - " u'|PENICILLIN|',\n", - " u'|CPD0-2358|']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ecoli.all_modulators()[0:10]" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-transported-chemicals\n", - "(all-transported-chemicals :primary-only? nil)\n", - "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil))\n", - "all-transported-chemicals\n", - "(all-transported-chemicals :primary-only? t)\n", - "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? t))\n", - "all-transported-chemicals\n", - "(all-transported-chemicals :primary-only? nil :from-compartment '|CCO-CYTOSOL|)\n", - "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :from-compartment '|CCO-CYTOSOL|))\n", - "all-transported-chemicals\n", - "(all-transported-chemicals :primary-only? nil :to-compartment '|CCO-CYTOSOL|)\n", - "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :to-compartment '|CCO-CYTOSOL|))\n", - "all-transported-chemicals\n", - "(all-transported-chemicals :primary-only? nil :show-compartment 'cell)\n", - "(with-organism (:org-id '|ECOLI|) (all-transported-chemicals :primary-only? nil :show-compartment 'cell))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|LI+|',\n", - " u'|MELIBIOSE|',\n", - " u'|D-GALACTURONATE|',\n", - " u'|PROTON|',\n", - " u'|CPD0-2241|',\n", - " u'|GUANINE|',\n", - " u'|Nucleosides|',\n", - " u'|CPD-20888|',\n", - " u'|XANTHINE|',\n", - " u'|N-ACETYL-D-MANNOSAMINE-6P|']" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "from-compartment\n", @@ -428,47 +282,9 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-protein-complexes\n", - "(all-protein-complexes :filter :all)\n", - "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n", - "all-protein-complexes\n", - "(all-protein-complexes :filter :hetero)\n", - "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :hetero))\n", - "all-protein-complexes\n", - "(all-protein-complexes :filter :homo)\n", - "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :homo))\n", - "all-protein-complexes\n", - "(all-protein-complexes :filter :all)\n", - "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|CPLX0-7660|',\n", - " u'|CPLX0-8247|',\n", - " u'|CPLX0-3102|',\n", - " u'|ACETYL-COA-CARBOXYLTRANSFER-CPLX|',\n", - " u'|CPLX0-7|',\n", - " u'|TRANS-CPLX-204|',\n", - " u'|FLAGELLAR-MOTOR-COMPLEX|',\n", - " u'|1-PFK|',\n", - " u'|CPLX0-8125|',\n", - " u'|CPLX0-7687|']" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "filter\n", @@ -491,41 +307,9 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-transcription-factors\n", - "(all-transcription-factors :allow-modified-forms? t)\n", - "(with-organism (:org-id '|ECOLI|) (all-transcription-factors :allow-modified-forms? t))\n", - "all-transcription-factors\n", - "(all-transcription-factors :allow-modified-forms? t)\n", - "(with-organism (:org-id '|ECOLI|) (all-transcription-factors :allow-modified-forms? t))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|G6165-MONOMER|',\n", - " u'|PHOSPHO-NARP|',\n", - " u'|G6882-MONOMER|',\n", - " u'|MONOMER0-1|',\n", - " u'|G7947-MONOMER|',\n", - " u'|G6175-MONOMER|',\n", - " u'|EG11554-MONOMER|',\n", - " u'|PD01196|',\n", - " u'|EG10087-MONOMER|',\n", - " u'|EG10226-MONOMER|']" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "Side-Effects\n", @@ -542,38 +326,9 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-genetic-regulation-proteins\n", - "(all-genetic-regulation-proteins :class '|Regulation| :allow-modified-forms? nil)\n", - "(with-organism (:org-id '|ECOLI|) (all-genetic-regulation-proteins :class '|Regulation| :allow-modified-forms? nil))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|G6165-MONOMER|',\n", - " u'|NARP-MONOMER|',\n", - " u'|TAR-CPLX|',\n", - " u'|G6882-MONOMER|',\n", - " u'|EG11140-MONOMER|',\n", - " u'|EG10881-MONOMER|',\n", - " u'|G7947-MONOMER|',\n", - " u'|G6175-MONOMER|',\n", - " u'|EG12111-MONOMER|',\n", - " u'|EG11554-MONOMER|']" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "class\n", @@ -590,123 +345,27 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-sigma-factors\n", - "(all-sigma-factors )\n", - "(with-organism (:org-id '|ECOLI|) (all-sigma-factors ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|EG11355-MONOMER|',\n", - " u'|RPOE-MONOMER|',\n", - " u'|RPOD-MONOMER|',\n", - " u'|RPON-MONOMER|',\n", - " u'|PD00440|',\n", - " u'|RPOS-MONOMER|',\n", - " u'|RPOH-MONOMER|']" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ecoli.all_sigma_factors()" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-operons\n", - "(all-operons )\n", - "(with-organism (:org-id '|ECOLI|) (all-operons ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|TU0-8814|'],\n", - " [u'|TU0-8710|'],\n", - " [u'|TU0-13847|'],\n", - " [u'|TU0-13769|'],\n", - " [u'|TU0-13667|'],\n", - " [u'|TU00321|'],\n", - " [u'|TU0-13385|'],\n", - " [u'|TU00223|'],\n", - " [u'|TU0-14243|'],\n", - " [u'|TU0-14168|']]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ecoli.all_operons()[0:10]" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::enzyme )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::enzyme ))\n", - "rxns-w-isozymes\n", - "(rxns-w-isozymes :rxns '(|DCYSDESULF-RXN| |RXN-11837| |RXN-14142| |DIHYDROOROTATE-DEHYDROGENASE-RXN| |RXN-12402| |RXN0-5285| |GLUCOSE-1-PHOSPHAT-RXN| |INOSINE-NUCLEOSIDASE-RXN| |RXN0-6509| |RXN0-6575| |RXN0-7167| |GLYCOGENSYN-RXN| |PUTTRANSAM-RXN| |2.7.10.1-RXN| |5.99.1.2-RXN| |1.5.1.34-RXN| |DHDOGALDOL-RXN| |RXN-19777| |RXN0-1661| |RXN0-6975| |RXN0-5364| |RXN-12073| |RXN-14285| |RXN-18999| |RXN-17780| |GLUTRACE-RXN| |KETOACYLCOATHIOL-RXN| |3.1.13.5-RXN| |QUINOPRIBOTRANS-RXN| |RXN0-6734| |RXN0-7251| |RXN-11635| |DIHYDROXYMETVALDEHYDRAT-RXN| |3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN| 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(rxns-catalyzed-by-complex ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|DCYSDESULF-RXN|',\n", - " u'|RXN-14142|',\n", - " u'|RXN-12402|',\n", - " u'|GLUCOSE-1-PHOSPHAT-RXN|',\n", - " u'|PUTTRANSAM-RXN|',\n", - " u'|1.5.1.34-RXN|',\n", - " u'|DHDOGALDOL-RXN|',\n", - " u'|RXN-19777|',\n", - " u'|RXN-12073|',\n", - " u'|RXN-14285|']" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxns\n", @@ -777,53 +395,9 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-enzymes\n", - "(all-enzymes )\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes ))\n", - "all-enzymes\n", - "(all-enzymes :type :any)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :any))\n", - "all-enzymes\n", - "(all-enzymes :type :chemical-change)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :chemical-change))\n", - "all-enzymes\n", - "(all-enzymes :type :small-molecule)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :small-molecule))\n", - "all-enzymes\n", - "(all-enzymes :type :transport)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :transport))\n", - "all-enzymes\n", - "(all-enzymes :type :non-transport)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :non-transport))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|MHPELY-MONOMER|',\n", - " u'|G6571-MONOMER|',\n", - " u'|G7751-MONOMER|',\n", - " u'|G7910-MONOMER|',\n", - " u'|G6904-MONOMER|',\n", - " u'|PGLUCONDEHYDRAT-MONOMER|',\n", - " u'|MONOMER0-1241|',\n", - " u'|ACECITLY-CPLX|',\n", - " u'|G7422-MONOMER|',\n", - " u'|EG12069-MONOMER|']" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "type\n", @@ -858,38 +432,9 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-transporters\n", - "(all-transporters )\n", - "(with-organism (:org-id '|ECOLI|) (all-transporters ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|DCUA-MONOMER|',\n", - " u'|G7399-MONOMER|',\n", - " u'|YIDT-MONOMER|',\n", - " u'|CORA-MONOMER|',\n", - " u'|EG12134-MONOMER|',\n", - " u'|EG11486-MONOMER|',\n", - " u'|CYNX-MONOMER|',\n", - " u'|YJDL-MONOMER|',\n", - " u'|EG11512-MONOMER|',\n", - " u'|GLTP-MONOMER|']" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ecoli.all_transporters()[0:10]" ] diff --git a/pythoncyc/PGDB.py b/pythoncyc/PGDB.py index c55b224..631641d 100644 --- a/pythoncyc/PGDB.py +++ b/pythoncyc/PGDB.py @@ -54,7 +54,7 @@ def may_be_frameid(obj): elif isinstance(obj, str): return Symbol(obj) else: - raise PythonCycError('Error: the argument must a string or a PFrame, but given {0}.'.format(x)) + raise PythonCycError('Error: the argument must a string or a PFrame, but given {0}.'.format(obj)) def mkey(obj): """ From 36c6b700e485077ca819a8abc559b153f6521ed3 Mon Sep 17 00:00:00 2001 From: glucksfall Date: Sun, 14 Apr 2019 01:13:43 -0400 Subject: [PATCH 09/17] updated examples --- .gitignore | 2 + .../Operations_on_Compounds-checkpoint.ipynb} | 155 +- ...ns_on_Enzymatic-Reactions-checkpoint.ipynb | 268 + .../Operations_on_Genes-checkpoint.ipynb} | 265 +- .../Operations_on_Pathways-checkpoint.ipynb | 397 + ...ins_and_Protein_Complexes-checkpoint.ipynb | 943 + .../Operations_on_Reactions-checkpoint.ipynb | 764 + ...ions_on_Regulation_Frames-checkpoint.ipynb | 1011 + .../enumeration_operations-checkpoint.ipynb} | 396 +- examples/Operations_on_Compounds.ipynb | 289 + .../Operations_on_Enzymatic-Reactions.ipynb | 268 + examples/Operations_on_Genes.ipynb | 608 + examples/Operations_on_Pathways.ipynb | 397 + ...ns_on_Proteins_and_Protein_Complexes.ipynb | 943 + examples/Operations_on_Reactions.ipynb | 764 + .../Operations_on_Regulation_Frames.ipynb | 1011 + examples/enumeration_operations.ipynb | 705 + ... - Operations on Enzymatic-Reactions.ipynb | 34762 ---- .../ptools API - Operations on Pathways.ipynb | 11390 -- ...ns on Proteins and Protein Complexes.ipynb | 1277 - ...ptools API - Operations on Reactions.ipynb | 122770 --------------- ...PI - Operations on Regulation Frames.ipynb | 1411 - pythoncyc/PTools.py | 2 +- 23 files changed, 8776 insertions(+), 172022 deletions(-) create mode 100644 .gitignore rename examples/{ptools API - Operations on Compounds.ipynb => .ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb} (57%) create mode 100644 examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb rename examples/{ptools API - Operations on Genes.ipynb => .ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb} (50%) create mode 100644 examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb create mode 100644 examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb create mode 100644 examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb create mode 100644 examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb rename examples/{ptools API - enumeration operations.ipynb => .ipynb_checkpoints/enumeration_operations-checkpoint.ipynb} (58%) create mode 100644 examples/Operations_on_Compounds.ipynb create mode 100644 examples/Operations_on_Enzymatic-Reactions.ipynb create mode 100644 examples/Operations_on_Genes.ipynb create mode 100644 examples/Operations_on_Pathways.ipynb create mode 100644 examples/Operations_on_Proteins_and_Protein_Complexes.ipynb create mode 100644 examples/Operations_on_Reactions.ipynb create mode 100644 examples/Operations_on_Regulation_Frames.ipynb create mode 100644 examples/enumeration_operations.ipynb delete mode 100644 examples/ptools API - Operations on Enzymatic-Reactions.ipynb delete mode 100644 examples/ptools API - Operations on Pathways.ipynb delete mode 100644 examples/ptools API - Operations on Proteins and Protein Complexes.ipynb delete mode 100644 examples/ptools API - Operations on Reactions.ipynb delete mode 100644 examples/ptools API - Operations on Regulation Frames.ipynb diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9fc9476 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*pyc +__pycache__ diff --git a/examples/ptools API - Operations on Compounds.ipynb b/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb similarity index 57% rename from examples/ptools API - Operations on Compounds.ipynb rename to examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb index 1291a63..8de4802 100644 --- a/examples/ptools API - Operations on Compounds.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb @@ -4,25 +4,18 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "#to run the script, you need to start pathway tools form the command line \n", "# using the -lisp -python options. Example (from the pathway tools github repository)\n", "import os\n", "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" ] }, { @@ -33,7 +26,16 @@ { "data": { "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" ] }, "execution_count": 2, @@ -45,54 +47,33 @@ "# modify sys.path to recognize local pythoncyc\n", "import os\n", "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", "\n", "sys.path" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", - "[u'|META|', u'|ECOLI|']\n", - "class-name-p\n", - "(class-name-p \"compounds\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"compounds\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Compounds| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Compounds| ))\n", - "get-class\n", - "(get-class |Compounds| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Compounds| ))\n", - "class-name-p\n", - "(class-name-p \"reactions\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"reactions\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Reactions| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Reactions| ))\n", - "get-class\n", - "(get-class |Reactions| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Reactions| ))\n", - "all-enzymes\n", - "(all-enzymes :type :chemical-change)\n", - "(with-organism (:org-id '|ECOLI|) (all-enzymes :type :chemical-change))\n" + "['|META|', '|ECOLI|']\n" ] } ], "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", "import pythoncyc\n", "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", + "print(all_orgids)\n", "\n", "meta = pythoncyc.select_organism(u'|META|')\n", "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", @@ -111,13 +92,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "reactions-of-compound\n", - "(reactions-of-compound '|CPD0-1107| :enzymatic? t)\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-compound '|CPD0-1107| :enzymatic? t))\n", - "reactions-of-compound\n", - "(reactions-of-compound '|CPD-8521| :enzymatic? t)\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-compound '|CPD-8521| :enzymatic? t))\n", - "[[u'|RXN0-5298|'], [u'|RXN0-1922|']]\n" + "[['|RXN0-5298|'], ['|RXN0-1922|']]\n" ] } ], @@ -147,17 +122,7 @@ "cell_type": "code", "execution_count": 5, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "substrate-of-generic-rxn?\n", - "(substrate-of-generic-rxn? '|CPD0-1107| '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrate-of-generic-rxn? '|CPD0-1107| '|DSBD-RXN| ))\n" - ] - } - ], + "outputs": [], "source": [ "try:\n", " lst = []\n", @@ -178,13 +143,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "pathways-of-compound\n", - "(pathways-of-compound '|CPD0-1107| )\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-compound '|CPD0-1107| ))\n", - "pathways-of-compound\n", - "(pathways-of-compound '|CPD-8521| )\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-compound '|CPD-8521| ))\n", - "[[u'|FUCCAT-PWY|', u'|FUC-RHAMCAT-PWY|'], []]\n" + "[['|FUCCAT-PWY|', '|FUC-RHAMCAT-PWY|'], []]\n" ] } ], @@ -216,17 +175,7 @@ "cell_type": "code", "execution_count": 7, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ACTIVATED-OR-INHIBITED-BY-COMPOUND\n", - "(ACTIVATED-OR-INHIBITED-BY-COMPOUND '|CPD0-1107| )\n", - "(with-organism (:org-id '|ECOLI|) (ACTIVATED-OR-INHIBITED-BY-COMPOUND '|CPD0-1107| ))\n" - ] - } - ], + "outputs": [], "source": [ "\"\"\"\n", "cpds\n", @@ -264,12 +213,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "tfs-bound-to-compound\n", - "(tfs-bound-to-compound '|CPD0-1107| :include-inactive? t)\n", - "(with-organism (:org-id '|ECOLI|) (tfs-bound-to-compound '|CPD0-1107| :include-inactive? t))\n", - "tfs-bound-to-compound\n", - "(tfs-bound-to-compound '|CPD-8521| :include-inactive? t)\n", - "(with-organism (:org-id '|ECOLI|) (tfs-bound-to-compound '|CPD-8521| :include-inactive? t))\n", "[[], []]\n" ] } @@ -283,30 +226,15 @@ }, { "cell_type": "code", - "execution_count": 26, - "metadata": { - "scrolled": false - }, + "execution_count": 9, + "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "full-enzyme-name\n", - "(full-enzyme-name '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (full-enzyme-name '|DSBD-RXN| ))\n", - "full-enzyme-name\n", - "(full-enzyme-name '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (full-enzyme-name '|RXN0-4342| ))\n", - "[u'dsbd-rxn', u'rxn0-4342']\n", - "\n", - "enzyme-activity-name\n", - "(enzyme-activity-name '|MHPELY-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-activity-name '|MHPELY-MONOMER| nil ))\n", - "enzyme-activity-name\n", - "(enzyme-activity-name '|G6571-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-activity-name '|G6571-MONOMER| nil ))\n", - "[u'4-hydroxy-2-oxovalerate aldolase', u'L,D-transpeptidase YcfS']\n" + "['dsbd-rxn', 'rxn0-4342']\n", + "['4-hydroxy-2-oxovalerate aldolase', 'L,D-transpeptidase YcfS']\n" ] } ], @@ -321,13 +249,12 @@ "lst = []\n", "for reaction in reactions:\n", " lst.append(ecoli.full_enzyme_name(reaction))\n", - "print lst[-10:]\n", - "print ''\n", + "print(lst[-10:])\n", "\n", "lst = []\n", "for enzyme in enzymes:\n", " lst.append(ecoli.enzyme_activity_name(enzyme))\n", - "print lst[-10:]" + "print(lst[-10:])" ] }, { @@ -340,21 +267,21 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 2", + "display_name": "Python 3", "language": "python", - "name": "python2" + "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" + "pygments_lexer": "ipython3", + "version": "3.6.7" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb new file mode 100644 index 0000000..05be910 --- /dev/null +++ b/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb @@ -0,0 +1,268 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " lst.append(ecoli.cofactors_and_pgroups_of_enzrxn(enzrxn = enzrxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "er\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "phys-relevant-only?\n", + "Optional If true, then only return activators that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_activators(enzrxn = enzrxn, phys_relevant_only=True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_inhibitors(enzrxn = enzrxn, phys_relevant_only = True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "include-super-pwys?\n", + "Keyword, Optional If non-nil, then not only will the direct pathways in which \n", + "enzrxn is associated in be returned, but also any enclosing super-pathways. If \n", + "enzrxn is associated with a reaction that is directly associated with a \n", + "super-pathway, then the function might return super-pathways even if this option \n", + "is nil.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.pathways_of_enzrxn(enzrxn = enzrxn, include_super_pwys = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "single-species\n", + "Optional An instance of the class |Organisms| If set, then enzrxn has the \n", + "further stricture that it must be an enzymatic reaction present in the organism \n", + "specified by the value passed to single‑species.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " for rxn1 in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " for rxn2 in ecoli.all_rxns(type_of_reactions = 'metab-smm'):\n", + " lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n", + " pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Genes.ipynb b/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb similarity index 50% rename from examples/ptools API - Operations on Genes.ipynb rename to examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb index 3a43670..1506a61 100644 --- a/examples/ptools API - Operations on Genes.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb @@ -4,25 +4,18 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "#to run the script, you need to start pathway tools form the command line \n", "# using the -lisp -python options. Example (from the pathway tools github repository)\n", "import os\n", "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" ] }, { @@ -33,7 +26,16 @@ { "data": { "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" ] }, "execution_count": 2, @@ -45,8 +47,12 @@ "# modify sys.path to recognize local pythoncyc\n", "import os\n", "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", "\n", "sys.path" ] @@ -60,26 +66,14 @@ "name": "stdout", "output_type": "stream", "text": [ - "[u'|META|', u'|ECOLI|']\n", - "class-name-p\n", - "(class-name-p \"genes\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"genes\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Genes| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Genes| ))\n", - "get-class\n", - "(get-class |Genes| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Genes| ))\n" + "['|META|', '|ECOLI|']\n" ] } ], "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", "import pythoncyc\n", "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", + "print(all_orgids)\n", "\n", "meta = pythoncyc.select_organism(u'|META|')\n", "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", @@ -95,13 +89,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "gene-p\n", - "(gene-p '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (gene-p '|EG11414| ))\n", - "gene-p\n", - "(gene-p '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (gene-p '|EG11127| ))\n", - "[u'|Genes|', u'|Genes|']\n" + "['|Genes|', '|Genes|']\n" ] } ], @@ -121,12 +109,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "enzymes-of-gene\n", - "(enzymes-of-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-gene '|EG11414| ))\n", - "enzymes-of-gene\n", - "(enzymes-of-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-gene '|EG11127| ))\n", "[[], []]\n" ] } @@ -147,13 +129,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "all-products-of-gene\n", - "(all-products-of-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (all-products-of-gene '|EG11414| ))\n", - "all-products-of-gene\n", - "(all-products-of-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (all-products-of-gene '|EG11127| ))\n", - "[[u'|EG11414-MONOMER|', u'|CPLX0-7910|', u'|CPLX0-3803|'], [u'|EG11127-MONOMER|']]\n" + "[['|EG11414-MONOMER|', '|CPLX0-7910|', '|CPLX0-3803|'], ['|EG11127-MONOMER|']]\n" ] } ], @@ -173,12 +149,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "reactions-of-gene\n", - "(reactions-of-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-gene '|EG11414| ))\n", - "reactions-of-gene\n", - "(reactions-of-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-gene '|EG11127| ))\n", "[[], []]\n" ] } @@ -199,12 +169,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "pathways-of-gene\n", - "(pathways-of-gene '|EG11414| :include-super-pwys? t :include-gene-prod-as-substrate? t)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-gene '|EG11414| :include-super-pwys? t :include-gene-prod-as-substrate? t))\n", - "pathways-of-gene\n", - "(pathways-of-gene '|EG11127| :include-super-pwys? t :include-gene-prod-as-substrate? t)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-gene '|EG11127| :include-super-pwys? t :include-gene-prod-as-substrate? t))\n", "[[], []]\n" ] } @@ -225,13 +189,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "chromosome-of-gene\n", - "(chromosome-of-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-gene '|EG11414| ))\n", - "chromosome-of-gene\n", - "(chromosome-of-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-gene '|EG11127| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n" + "['|COLI-K12|', '|COLI-K12|']\n" ] } ], @@ -251,13 +209,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "unmodified-gene-product\n", - "(unmodified-gene-product '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-gene-product '|EG11414| ))\n", - "unmodified-gene-product\n", - "(unmodified-gene-product '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-gene-product '|EG11127| ))\n", - "[u'|EG11414-MONOMER|', u'|EG11127-MONOMER|']\n" + "['|EG11414-MONOMER|', '|EG11127-MONOMER|']\n" ] } ], @@ -277,13 +229,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "unmodified-gene-products\n", - "(unmodified-gene-products '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-gene-products '|EG11414| ))\n", - "unmodified-gene-products\n", - "(unmodified-gene-products '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-gene-products '|EG11127| ))\n", - "[[u'|EG11414-MONOMER|'], [u'|EG11127-MONOMER|']]\n" + "[['|EG11414-MONOMER|'], ['|EG11127-MONOMER|']]\n" ] } ], @@ -303,13 +249,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "next-gene-on-replicon\n", - "(next-gene-on-replicon '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (next-gene-on-replicon '|EG11414| ))\n", - "next-gene-on-replicon\n", - "(next-gene-on-replicon '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (next-gene-on-replicon '|EG11127| ))\n", - "[u'|EG10850|', u'|EG11024|']\n" + "['|EG10850|', '|EG11024|']\n" ] } ], @@ -329,13 +269,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "previous-gene-on-replicon\n", - "(previous-gene-on-replicon '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (previous-gene-on-replicon '|EG11414| ))\n", - "previous-gene-on-replicon\n", - "(previous-gene-on-replicon '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (previous-gene-on-replicon '|EG11127| ))\n", - "[u'|G7950|', u'|EG11126|']\n" + "['|G7950|', '|EG11126|']\n" ] } ], @@ -355,14 +289,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "genes are the same.\n", - "adjacent-genes?\n", - "(adjacent-genes? '|EG11414| '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (adjacent-genes? '|EG11414| '|EG11127| ))\n", - "adjacent-genes?\n", - "(adjacent-genes? '|EG11127| '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (adjacent-genes? '|EG11127| '|EG11414| ))\n", - "genes are the same.\n", + "both queries are the same.\n", + "both queries are the same.\n", "[None, False, False, None]\n" ] } @@ -384,14 +312,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "genes are the same.\n", - "neighboring-genes-p\n", - "(neighboring-genes-p '|EG11414| '|EG11127| 10 )\n", - "(with-organism (:org-id '|ECOLI|) (neighboring-genes-p '|EG11414| '|EG11127| 10 ))\n", - "neighboring-genes-p\n", - "(neighboring-genes-p '|EG11127| '|EG11414| 10 )\n", - "(with-organism (:org-id '|ECOLI|) (neighboring-genes-p '|EG11127| '|EG11414| 10 ))\n", - "genes are the same.\n", + "both queries are the same.\n", + "both queries are the same.\n", "[None, False, False, None]\n" ] } @@ -409,19 +331,10 @@ "execution_count": 16, "metadata": {}, "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "gene-clusters\n", - "(gene-clusters '(|EG11414| |EG11127|) 4000 )\n", - "(with-organism (:org-id '|ECOLI|) (gene-clusters '(|EG11414| |EG11127|) 4000 ))\n" - ] - }, { "data": { "text/plain": [ - "{u'|EG11127|': [u'|EG11414|']}" + "{'|EG11127|': ['|EG11414|']}" ] }, "execution_count": 16, @@ -437,17 +350,7 @@ "cell_type": "code", "execution_count": 17, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rna-coding-gene?\n", - "(rna-coding-gene? '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (rna-coding-gene? '|EG11414| ))\n" - ] - } - ], + "outputs": [], "source": [ "try:\n", " lst = []\n", @@ -462,17 +365,7 @@ "cell_type": "code", "execution_count": 18, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "protein-coding-gene?\n", - "(protein-coding-gene? '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (protein-coding-gene? '|EG11414| ))\n" - ] - } - ], + "outputs": [], "source": [ "try:\n", " lst = []\n", @@ -492,12 +385,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "pseudo-gene-p\n", - "(pseudo-gene-p '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (pseudo-gene-p '|EG11414| ))\n", - "pseudo-gene-p\n", - "(pseudo-gene-p '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (pseudo-gene-p '|EG11127| ))\n", "[False, False]\n" ] } @@ -518,12 +405,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "phantom-gene-p\n", - "(phantom-gene-p '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (phantom-gene-p '|EG11414| ))\n", - "phantom-gene-p\n", - "(phantom-gene-p '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (phantom-gene-p '|EG11127| ))\n", "[False, False]\n" ] } @@ -544,12 +425,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "dna-binding-site-p\n", - "(dna-binding-site-p '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (dna-binding-site-p '|EG11414| ))\n", - "dna-binding-site-p\n", - "(dna-binding-site-p '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (dna-binding-site-p '|EG11127| ))\n", "[False, False]\n" ] } @@ -570,12 +445,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "terminatorp\n", - "(terminatorp '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (terminatorp '|EG11414| ))\n", - "terminatorp\n", - "(terminatorp '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (terminatorp '|EG11127| ))\n", "[False, False]\n" ] } @@ -596,13 +465,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "operon-of-gene\n", - "(operon-of-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (operon-of-gene '|EG11414| ))\n", - "operon-of-gene\n", - "(operon-of-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (operon-of-gene '|EG11127| ))\n", - "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-36411|', u'|TU0-13193|']]\n" + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-36411|', '|TU0-13193|']]\n" ] } ], @@ -622,13 +485,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "genes-in-same-operon\n", - "(genes-in-same-operon '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-in-same-operon '|EG11414| ))\n", - "genes-in-same-operon\n", - "(genes-in-same-operon '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-in-same-operon '|EG11127| ))\n", - "[[u'|EG12115|', u'|EG10850|', u'|EG11414|'], [u'|EG11125|', u'|EG11126|', u'|EG11127|']]\n" + "[['|EG12115|', '|EG10850|', '|EG11414|'], ['|EG11125|', '|EG11126|', '|EG11127|']]\n" ] } ], @@ -648,13 +505,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "gene-transcription-units\n", - "(gene-transcription-units '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (gene-transcription-units '|EG11414| ))\n", - "gene-transcription-units\n", - "(gene-transcription-units '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (gene-transcription-units '|EG11127| ))\n", - "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-13193|']]\n" + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n" ] } ], @@ -674,13 +525,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "cotranscribed-genes\n", - "(cotranscribed-genes '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (cotranscribed-genes '|EG11414| ))\n", - "cotranscribed-genes\n", - "(cotranscribed-genes '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (cotranscribed-genes '|EG11127| ))\n", - "[[u'|EG12115|', u'|EG10850|'], [u'|EG11125|', u'|EG11126|']]\n" + "[['|EG12115|', '|EG10850|'], ['|EG11125|', '|EG11126|']]\n" ] } ], @@ -700,12 +545,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "terminators-affecting-gene\n", - "(terminators-affecting-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (terminators-affecting-gene '|EG11414| ))\n", - "terminators-affecting-gene\n", - "(terminators-affecting-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (terminators-affecting-gene '|EG11127| ))\n", "[[], []]\n" ] } @@ -726,13 +565,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "chromosome-of-object\n", - "(chromosome-of-object '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-object '|EG11414| ))\n", - "chromosome-of-object\n", - "(chromosome-of-object '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-object '|EG11127| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n" + "['|COLI-K12|', '|COLI-K12|']\n" ] } ], @@ -753,21 +586,21 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 2", + "display_name": "Python 3", "language": "python", - "name": "python2" + "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" + "pygments_lexer": "ipython3", + "version": "3.6.7" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb new file mode 100644 index 0000000..539ab4f --- /dev/null +++ b/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb @@ -0,0 +1,397 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|EG12082|',\n", + " '|EG12088|',\n", + " '|EG12090|',\n", + " '|EG12091|',\n", + " '|EG12092|',\n", + " '|EG11773|',\n", + " '|EG12093|',\n", + " '|EG12089|',\n", + " '|EG12087|',\n", + " '|EG11774|',\n", + " '|EG12086|',\n", + " '|EG12084|',\n", + " '|EG12083|',\n", + " '|EG10330|',\n", + " '|EG10331|',\n", + " '|EG10332|',\n", + " '|EG10333|']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "sorted?\n", + "Keyword, Optional If true, the genes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = 'all', base = True):\n", + " lst.append(ecoli.genes_of_pathway(pwy = pwy, sorted = True))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|NADH-DHI-CPLX|', '|FUMARATE-REDUCTASE|']" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "sorted?\n", + "Keyword, Optional If true, the enzymes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.enzymes_of_pathway(pwy = pwy, sorted = True, experimental_only = True))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|FUM|',\n", + " '|SUC|',\n", + " '|Menaquinones|',\n", + " '|Menaquinols|',\n", + " '|E-|',\n", + " '|PROTON|',\n", + " '|NAD|',\n", + " '|NADH|']" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.compounds_of_pathway(pwy = pwy))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NADH|',\n", + " '|Menaquinones|',\n", + " '|Menaquinols|',\n", + " '|PROTON|',\n", + " '|TRIMETHYLAMINE-N-O|'],\n", + " ['|TRIMETHYLAMINE-N-O|', '|NADH|'],\n", + " ['|NAD|',\n", + " '|Menaquinols|',\n", + " '|PROTON|',\n", + " '|TRIMETHYLAMINE|',\n", + " '|WATER|',\n", + " '|Menaquinones|'],\n", + " ['|WATER|', '|TRIMETHYLAMINE|', '|NAD|']]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.substrates_of_pathway(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[],\n", + " ['|PWY-7195|', '|PWY-6556|'],\n", + " ['|PWY0-1597|'],\n", + " ['|RIBOSYN2-PWY|'],\n", + " ['|PWY0-1295|', '|PWY-6556|'],\n", + " [],\n", + " ['|PWY0-1584|', '|PWY0-1581|', '|PWY0-1573|', '|PWY0-1352|'],\n", + " [],\n", + " [],\n", + " []]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.variants_of_pathway(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[['|RXN0-5264|', '|RXN0-5388|']], 1, 2, 2]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|, which is not a super-pathway (i.e., does \n", + "not have any entries in its 'sub‑pathways slot). \n", + "rxn-list\n", + "Optional The list of reactions to use as the starting list of connected \n", + "component clusters. Defaults to (get‑slot‑values pwy 'reaction‑list).\n", + "\n", + "pred-list\n", + "Optional The list of reaction predecessors to iterate from in order to cluster \n", + "the reactions in rxn‑list. Defaults to (get‑slot‑values pwy 'predecessors).\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.pathway_components(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, True, False, True, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.noncontiguous_pathway_p(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|DMKCYT-RXN|', '|RXN-15348|', False],\n", + " ['|DMKCYT-RXN|', '|LACTALDREDUCT-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|PFLDEACTIV-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|OHMETPYRKIN-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-7094|', False],\n", + " ['|DMKCYT-RXN|', '|TRIOSEPISOMERIZATION-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-7298|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-1137|', False],\n", + " ['|DMKCYT-RXN|', '|BADH-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|DMKCYT-RXN|', False]]" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn1\n", + "An instance of the class |Reactions|. \n", + "rxn2\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True)[0:10]:\n", + " for rxn1 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", + " for rxn2 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", + " lst.append([rxn1, rxn2, ecoli.rxns_adjacent_in_pwy_p(rxn1 = rxn1, rxn2 = rxn2, pwy = pwy)])\n", + "# lst.append(ecoli.rxns_adjacent_in_pwy_p(rxn1 = u'|RXN0-5264|', rxn2 = u'|RXN0-5388|', pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb new file mode 100644 index 0000000..cbe4808 --- /dev/null +++ b/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb @@ -0,0 +1,943 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "complexes = ecoli.all_protein_complexes()[0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", + "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "coefficients?\n", + "Keyword, Optional If true, then the second return value of the function will be \n", + "a list of monomer coefficients. Defaults to true. \n", + "unmodify?\n", + "Keyword, Optional If true, obtain the monomers of the unmodified form of p.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein, coefficients = True, unmodify = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", + "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "exclude-small-molecules?\n", + "Keyword, Optional If nil, then small molecule components are also returned. \n", + "Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein, exclude_small_molecules = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.containers_of(protein = protein, exclude_self = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, True]\n", + "[True, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|CPLX0-7660|', '|CPLX0-8247|']\n", + "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|CPLX0-7660|', '|CPLX0-8247|']\n", + "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "prots\n", + "A list of instances of the class |Proteins|. \n", + "debind?\n", + "Keyword, Optional When non-nil, the proteins are further simplified by obtaining \n", + "the unbound form of the protein, if it is bound to a small molecule. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein], debind = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein]))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_forms(protein = protein, all_variants = True, exclude_self= True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|CPLX0-3970|', '|ABC-22-CPLX|'], ['|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106|'], ['|EG12129|']]\n", + "[['|EG10676|'], ['|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106|'], ['|EG12129|']]\n", + "[['|EG10676|'], ['|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "kb\n", + "Keyword, Optional The KB object of the KB in which to find the associated \n", + "reactions. Defaults to the current PGDB. \n", + "include-specific-forms?\n", + "Keyword, Optional When true, specific forms of associated generic reactions are \n", + "also returned. Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein, include_subreactions = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|ECOLI|'], ['|ECOLI|']]\n", + "[['|ECOLI|'], ['|ECOLI|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, True]\n", + "[False, False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Optional Can take on one of the following values to select more precisely what \n", + "is meant by an “enzyme”:\n", + "\n", + ":any\n", + "Any protein that catalyzes a reaction is considered an enzyme. \n", + ":chemical-change\n", + "If the reactants and products of the catalyzed reactin differ, and not just by \n", + "their cellular location, then the protein is considered an enzyme. \n", + ":small-molecule\n", + "If the reactants of the catalyzed reaction differ and are small molecules, then \n", + "the protein is considered an enzyme. \n", + ":transport\n", + "If the protein catalyzes a transport reaction. \n", + ":non-transport\n", + "If the protein only catalyzes non-transport reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'any'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'non-transport-non-pathway'))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in complexes:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|Proteins|', '|Proteins|']\n", + "['|Proteins|', '|Proteins|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|Protein-Complexes|', '|Protein-Complexes|']\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "check-protein-components?\n", + "Optional If true, check all components of this protein for catalyzed reactions. \n", + "Defaults to true. \n", + "check-protein-containers?\n", + "Optional If true, check the containers and modified forms of the protein for \n", + "catalyzed reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_containers = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_components = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n", + "['|CCI-CYTOSOL-GN|', False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = 'CCO-CYTOSOL'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = ['CCO-CYTOSOL', 'CCO-MEMBRANE']))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|MTR-MONOMER|', '|G7942-MONOMER|', '|NANT-MONOMER|', '|B1006-MONOMER|', '|YDHE-MONOMER|', '|YDEA-MONOMER|', '|PITA-MONOMER|', '|YEIM-MONOMER|', '|BCR-MONOMER|', '|YGFO-MONOMER|']\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "membranes\n", + "Keyword Either :all or a list of instances of the class. Defaults to :all \n", + "'CCO‑MEMBRANE. \n", + "method\n", + "Either :location or :reaction‑compartments. :location will check the 'locations \n", + "slot, while :reaction‑compartments will examine the compartments of reaction \n", + "substrates. Default value is :location. \n", + "\"\"\"\n", + "\n", + "lst = ecoli.all_transporters_across(membranes = 'all')\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb new file mode 100644 index 0000000..a31329a --- /dev/null +++ b/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb @@ -0,0 +1,764 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|G6350|'],\n", + " ['|EG10754|'],\n", + " [],\n", + " [],\n", + " [],\n", + " ['|EG10068|'],\n", + " ['|EG10278|', '|G7213|'],\n", + " [],\n", + " ['|G7590|'],\n", + " []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.genes_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NICOTINATE_NUCLEOTIDE|', '|ATP|', '|PROTON|', '|PPI|', '|DEAMIDO-NAD|'],\n", + " ['|ACETALD|', '|PYRUVATE|', '|PROTON|', '|ACETOIN|', '|CARBON-DIOXIDE|'],\n", + " ['|Protein-Red-Disulfides|',\n", + " '|MONOMER0-4152|',\n", + " '|MONOMER0-4438|',\n", + " '|Protein-Ox-Disulfides|'],\n", + " ['|PROTON|', '|AMINO-OXOBUT|', '|AMINO-ACETONE|', '|CARBON-DIOXIDE|'],\n", + " ['|Cytochromes-B-Reduced|', '|Cytochromes-B|', '|Reduced-Cytochromes-o|'],\n", + " ['|ATP|',\n", + " '|L-CITRULLINE|',\n", + " '|L-ASPARTATE|',\n", + " '|PROTON|',\n", + " '|L-ARGININO-SUCCINATE|',\n", + " '|PPI|',\n", + " '|AMP|'],\n", + " ['|ACETYL-COA|', '|CPD-7221|', '|CPD-15244|', '|CO-A|'],\n", + " ['|MONOMER0-1641|', '|TORR-CPLX|', '|CPLX0-2821|'],\n", + " ['|ATP|',\n", + " '|D-BETA-D-HEPTOSE-1-P|',\n", + " '|PROTON|',\n", + " '|ADP-D-GLYCERO-D-MANNO-HEPTOSE|',\n", + " '|PPI|'],\n", + " ['|DSBD-MONOMER|', '|CPLX0-8004|', '|DSBG-MONOMER|', '|DSBDOXI-MONOMER|']]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.substrates_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NICONUCADENYLYLTRAN-MONOMER|'],\n", + " ['|PYRUVOXID-CPLX|'],\n", + " [],\n", + " [],\n", + " [],\n", + " ['|CPLX0-238|'],\n", + " ['|G7213-MONOMER|', '|FADA-CPLX|'],\n", + " [],\n", + " ['|CPLX0-3661|'],\n", + " []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. Default value \n", + "is nil. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "local-only-p\n", + "Keyword, Optional When true, only return enzymes that catalyze the specific form \n", + "of the reaction, as opposed to enzymes that are known to catalyze a more general \n", + "form (i.e., class) of the reaction. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzymes_of_reaction(rxn = rxn, species = u'|ECOLI|', \n", + " experimental_only = False, local_only_p = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[['|PROTON|', '|ATP|', '|NICOTINATE_NUCLEOTIDE|'],\n", + " ['|PPI|', '|DEAMIDO-NAD|']],\n", + " [['|PROTON|', '|PYRUVATE|', '|ACETALD|'], ['|ACETOIN|', '|CARBON-DIOXIDE|']],\n", + " [['|MONOMER0-4152|', '|Protein-Red-Disulfides|'],\n", + " ['|MONOMER0-4438|', '|Protein-Ox-Disulfides|']],\n", + " [['|AMINO-OXOBUT|', '|PROTON|'], ['|AMINO-ACETONE|', '|CARBON-DIOXIDE|']],\n", + " [['|Cytochromes-B-Reduced|', '|Cytochromes-B|'],\n", + " ['|Cytochromes-B|', '|Reduced-Cytochromes-o|']],\n", + " [['|L-ASPARTATE|', '|L-CITRULLINE|', '|ATP|'],\n", + " ['|PROTON|', '|L-ARGININO-SUCCINATE|', '|PPI|', '|AMP|']],\n", + " [['|CPD-15244|', '|CO-A|'], ['|CPD-7221|', '|ACETYL-COA|']],\n", + " None,\n", + " [['|PROTON|', '|D-BETA-D-HEPTOSE-1-P|', '|ATP|'],\n", + " ['|ADP-D-GLYCERO-D-MANNO-HEPTOSE|', '|PPI|']],\n", + " None]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "direction\n", + "Keyword, Optional Can take on the following values:\n", + "\n", + ":L2R\n", + "The reaction direction goes from ‘left to right’, as described in the \n", + "|Reactions| instance. \n", + ":R2L\n", + "The reaction direction goes from ‘right to left’; the opposite of what is \n", + "described in the |Reactions| instance. \n", + "\n", + "pwy\n", + "Keyword, Optional An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.reaction_reactants_and_products(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|SMALL-MOLECULE|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.reaction_type(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_without_sequenced_enzyme_p\u001b[0;34m(self, rxn)\u001b[0m\n\u001b[1;32m 1111\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1112\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1113\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1115\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "complete?\n", + "Optional If true, the predicate will return true when there is any associated \n", + "gene without a sequence. If nil, the predicate will return true when all \n", + "associated genes are without a sequence. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_without_sequenced_enzyme_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is REACTION-WITHOUT-SEQUENCED-ENZYME-P, \n", + "# which only argument is a rxn" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "hole-if-any-gene-without-position?\n", + "Keyword, Optional If true, then genes without specified coordinates for the \n", + "current organism’s genome are not counted when determining the status of the \n", + "reaction.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.pathway_hole_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1139\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1140\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1141\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1142\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1143\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_present_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is RXN-PRESENT?" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "specific-rxn\n", + "A child of the class |Reactions|. \n", + "generic-rxn\n", + "A child of the class |Reactions|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_specific_form_of_rxn_p(specific_rxn = rxn, generic_rxn = u'|RXN0-3741|'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.nonspecific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.specific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_in_compartment_p(rxn = rxn, compartments = [u'|CCO_CYTOSOL|']))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1240\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCell\u001b[0m \u001b[0mCompartment\u001b[0m \u001b[0mOntology\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1241\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1242\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1244\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "default\n", + "Optional The default compartment for reactions without any compartment \n", + "annotations on their substrates. The default value is 'CCO‑CYTOSOL. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.compartment_of_rxn(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is missing (?)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-PERI-BAC|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-PERI-BAC|']]" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "sides\n", + "Keyword, Optional The slots of the reaction to consider. The default value is \n", + "'(LEFT RIGHT). \n", + "default-compartment\n", + "The default compartment, as determined by the function (default‑compartment), \n", + "which currently is set to 'CCO‑CYTOSOL.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.compartments_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|Nucleosides|'],\n", + " ['|D-ALANINE|', '|PROTON|'],\n", + " ['|GUANINE|'],\n", + " ['|DEOXYINOSINE|', '|PROTON|'],\n", + " ['|PROTON|', '|CPD0-2241|'],\n", + " ['|Inorganic-Compounds|'],\n", + " ['|PROTON|', '|D-GALACTURONATE|'],\n", + " ['|CPD0-2486|'],\n", + " ['|MELIBIOSE|', '|LI+|'],\n", + " ['|FORMATE|']]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "side\n", + "Keyword, Optional The side of the reaction from which to return the transported \n", + "compound. \n", + "primary-only?\n", + "Keyword, Optional If true, then filter out common exchangers (currently defined \n", + "as '(PROTON NA CPD-1)+). If true, and the only transported compounds are in this \n", + "list, then the filter doesn’t apply. \n", + "from-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported from that compartment. \n", + "to-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported to that compartment. \n", + "show-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, and the \n", + "compound is modified during transport, then only return the form of the compound \n", + "as found in this compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':transport'):\n", + " lst.append(ecoli.transported_chemicals(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.get_predecessors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.get_successors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, True, False, False, False]" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_w_isozymes_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb new file mode 100644 index 0000000..55f94a3 --- /dev/null +++ b/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb @@ -0,0 +1,1011 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "\n", + "regs = [x.frameid for x in ecoli.regulation.instances][0:2]\n", + "genes = [x.frameid for x in ecoli.genes.instances][0:2]\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "tus = [x.frameid for x in ecoli.transcription_units.instances][0:2]\n", + "dna_sites = [x.frameid for x in ecoli.DNA_Binding_Sites.instances][0:2]\n", + "mrna_sites = [x.frameid for x in ecoli.mRNA_Binding_Sites.instances][0:2]\n", + "terminators = [x.frameid for x in ecoli.Terminators.instances][0:2]\n", + "promoters = [x.frameid for x in ecoli.Promoters.instances][0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.activation_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.inhibition_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_activators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_inhibitors(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_p(protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.regulator_of_type(protein, class_name = ':activator'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.regulon_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU162|'], ['|TU461|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.regulation_frame_transcription_units(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|REG0-11053|', '|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_regulation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|REG0-11053|', '|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibition_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_units_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_regulated_by_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.DNA_binding_sites_of_protein(protein, all_forms = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulator_proteins_of_transcription_unit(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_ligands(protein, u':both'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_active_forms(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|G6761|', '|EG10457|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulating_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulated_by_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[None, None, None], [['|G6761-MONOMER|'], ['|PD00288|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.regulators_of_gene_transcription(gene, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibitors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[None, None, None], [None, ['|PD01379|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulators_of_operon_transcription(tu, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[None, '|PM0-8720|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_promoter(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6954|'], ['|EG11346|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_genes(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|G6954|', '|EG11346|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_first_gene(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|BS0-8048|', '|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_transcription_factors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_mrna_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.chromosome_of_operon(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|BS0-7937|', '|BS0-7936|', '|BS0-7935|', '|BS0-7225|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_sites_affecting_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_site_to_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|PHOSPHO-PHOB|'], ['|CPLX0-7639|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_to_regulators(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-13975|'], ['|TU0-8636|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.transcription_units_of_promoter(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.promoter_binding_sites(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_terminators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-8814|'], ['|TU0-8340|']]\n", + "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n", + "[['|TU0-2021|'], ['|TU0-13514|']]\n", + "[['|TU0-13975|'], ['|TU0-8636|']]\n", + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n", + "[['|TU-8390|', '|TU-8389|'], ['|TU00091|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|PM0-2201|'], ['|PM0-9620|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_promoters(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6954|'], ['|PM0-8720|', '|EG11346|', '|BS0-8048|', '|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_all_components(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-2021|'], ['|TU0-13514|']]\n", + "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(dna_site))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for mrna_site in mrna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(mrna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - enumeration operations.ipynb b/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb similarity index 58% rename from examples/ptools API - enumeration operations.ipynb rename to examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb index 7968ef8..95419ac 100644 --- a/examples/ptools API - enumeration operations.ipynb +++ b/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb @@ -27,17 +27,15 @@ "data": { "text/plain": [ "['',\n", - " '/usr/lib/python2.7',\n", - " '/usr/lib/python2.7/plat-x86_64-linux-gnu',\n", - " '/usr/lib/python2.7/lib-tk',\n", - " '/usr/lib/python2.7/lib-old',\n", - " '/usr/lib/python2.7/lib-dynload',\n", - " '/usr/local/lib/python2.7/dist-packages',\n", - " '/usr/lib/python2.7/dist-packages',\n", - " '/usr/lib/python2.7/dist-packages/gtk-2.0',\n", - " '/usr/local/lib/python2.7/dist-packages/IPython/extensions',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", " '/home/glucksfall/.ipython',\n", - " '/shared/D1/opt/github-repositories/PythonCyc.networkbiolab']" + " '/opt/github-repositories/PythonCyc.networkbiolab']" ] }, "execution_count": 2, @@ -68,14 +66,14 @@ "name": "stdout", "output_type": "stream", "text": [ - "[u'|META|', u'|ECOLI|']\n" + "['|META|', '|ECOLI|']\n" ] } ], "source": [ "import pythoncyc\n", "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", + "print(all_orgids)\n", "\n", "meta = pythoncyc.select_organism(u'|META|')\n", "ecoli = pythoncyc.select_organism(u'|ECOLI|')" @@ -89,16 +87,16 @@ { "data": { "text/plain": [ - "[u'|PWY0-1347|',\n", - " u'|PWY-6690|',\n", - " u'|PWY0-1348|',\n", - " u'|PWY-5162|',\n", - " u'|PWY0-1352|',\n", - " u'|PWY0-1355|',\n", - " u'|2PHENDEG-PWY|',\n", - " u'|PWY0-1465|',\n", - " u'|TRESYN-PWY|',\n", - " u'|PANTO-PWY|']" + "['|PWY0-1347|',\n", + " '|PWY-6690|',\n", + " '|PWY0-1348|',\n", + " '|PWY-5162|',\n", + " '|PWY0-1352|',\n", + " '|PWY0-1355|',\n", + " '|2PHENDEG-PWY|',\n", + " '|PWY0-1465|',\n", + " '|TRESYN-PWY|',\n", + " '|PANTO-PWY|']" ] }, "execution_count": 4, @@ -129,16 +127,16 @@ { "data": { "text/plain": [ - "[u'|RXN-17635|',\n", - " u'|RXN-6268|',\n", - " u'|RXN-7282|',\n", - " u'|RXN-10720|',\n", - " u'|RXN-12870|',\n", - " u'|RXN-14515|',\n", - " u'|RXN-13460|',\n", - " u'|RXN-14808|',\n", - " u'|RXN-18819|',\n", - " u'|RXN-15121|']" + "['|RXN-17635|',\n", + " '|RXN-6268|',\n", + " '|RXN-7282|',\n", + " '|RXN-10720|',\n", + " '|RXN-12870|',\n", + " '|RXN-14515|',\n", + " '|RXN-13460|',\n", + " '|RXN-14808|',\n", + " '|RXN-18819|',\n", + " '|RXN-15121|']" ] }, "execution_count": 5, @@ -200,28 +198,27 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[u'|RXN-17635|']\n" + "['|RXN-17635|']\n" ] }, { - "ename": "PythonCycError", - "evalue": "Error: the argument must a string or a PFrame, but given |RXN-17635|.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mPythonCycError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 4\u001b[0m \"\"\"\n\u001b[1;32m 5\u001b[0m \u001b[0;32mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'spontaneous'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_substrates\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'|RXN-17635|'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;31m#rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1][0])\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m/shared/D1/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.pyc\u001b[0m in \u001b[0;36mall_substrates\u001b[0;34m(self, rxns)\u001b[0m\n\u001b[1;32m 754\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mleft\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mright\u001b[0m \u001b[0mslots\u001b[0m \u001b[0mof\u001b[0m \u001b[0ma\u001b[0m \u001b[0mreaction\u001b[0m \u001b[0mframe\u001b[0m \u001b[0mcan\u001b[0m \u001b[0mcontain\u001b[0m \u001b[0mstrings\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 755\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 756\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallList\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'all-substrates'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 757\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 758\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mall_cofactors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.pyc\u001b[0m in \u001b[0;36mmay_be_frameid\u001b[0;34m(obj)\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mSymbol\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 56\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 57\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPythonCycError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Error: the argument must a string or a PFrame, but given {0}.'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 58\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 59\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mmkey\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPythonCycError\u001b[0m: Error: the argument must a string or a PFrame, but given |RXN-17635|." - ] + "data": { + "text/plain": [ + "['|Protein-Arginine-Aminocarbinol|',\n", + " '|PROTON|',\n", + " '|Protein-Arginine-Imidazolidine|']" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ @@ -230,32 +227,92 @@ "A list of reaction frames. \n", "\"\"\"\n", "print(ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])\n", - "ecoli.all_substrates(u'|RXN-17635|')#rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1][0])" + "ecoli.all_substrates(rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|DIPYRROMETHANE|',\n", + " '|GTP|',\n", + " '|UBIQUINONE-8|',\n", + " '|AMMONIUM|',\n", + " '|LYS|',\n", + " '|HEME_O|',\n", + " '|CPD-18260|',\n", + " '|PQQ|',\n", + " '|SIROHEME|',\n", + " '|Mo-molybdopterin-cofactor|']" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ecoli.all_cofactors()[0:10]" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|DEOXY-RIBOSE-1P|',\n", + " '|CPD0-1546|',\n", + " '|CPD0-1545|',\n", + " '|NACL|',\n", + " '|Gramicidins|',\n", + " '|CPD0-1633|',\n", + " '|G7642-MONOMER|',\n", + " '|CPD-9229|',\n", + " '|PENICILLIN|',\n", + " '|CPD0-2358|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ecoli.all_modulators()[0:10]" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|LI+|',\n", + " '|MELIBIOSE|',\n", + " '|D-GALACTURONATE|',\n", + " '|PROTON|',\n", + " '|CPD0-2241|',\n", + " '|GUANINE|',\n", + " '|Nucleosides|',\n", + " '|CPD-20888|',\n", + " '|XANTHINE|',\n", + " '|N-ACETYL-D-MANNOSAMINE-6P|']" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "from-compartment\n", @@ -282,9 +339,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|CPLX0-7660|',\n", + " '|CPLX0-8247|',\n", + " '|CPLX0-3102|',\n", + " '|ACETYL-COA-CARBOXYLTRANSFER-CPLX|',\n", + " '|CPLX0-7|',\n", + " '|TRANS-CPLX-204|',\n", + " '|FLAGELLAR-MOTOR-COMPLEX|',\n", + " '|1-PFK|',\n", + " '|CPLX0-8125|',\n", + " '|CPLX0-7687|']" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "filter\n", @@ -307,9 +384,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|G6165-MONOMER|',\n", + " '|PHOSPHO-NARP|',\n", + " '|G6882-MONOMER|',\n", + " '|MONOMER0-1|',\n", + " '|G7947-MONOMER|',\n", + " '|G6175-MONOMER|',\n", + " '|EG11554-MONOMER|',\n", + " '|PD01196|',\n", + " '|EG10087-MONOMER|',\n", + " '|EG10226-MONOMER|']" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "Side-Effects\n", @@ -326,9 +423,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|G6165-MONOMER|',\n", + " '|NARP-MONOMER|',\n", + " '|TAR-CPLX|',\n", + " '|G6882-MONOMER|',\n", + " '|EG11140-MONOMER|',\n", + " '|EG10881-MONOMER|',\n", + " '|G7947-MONOMER|',\n", + " '|G6175-MONOMER|',\n", + " '|EG12111-MONOMER|',\n", + " '|EG11554-MONOMER|']" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "class\n", @@ -345,27 +462,84 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 13, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|EG11355-MONOMER|',\n", + " '|RPOE-MONOMER|',\n", + " '|RPOD-MONOMER|',\n", + " '|RPON-MONOMER|',\n", + " '|PD00440|',\n", + " '|RPOS-MONOMER|',\n", + " '|RPOH-MONOMER|']" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ecoli.all_sigma_factors()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[['|TU0-8814|'],\n", + " ['|TU0-8710|'],\n", + " ['|TU0-13847|'],\n", + " ['|TU0-13769|'],\n", + " ['|TU0-13667|'],\n", + " ['|TU00321|'],\n", + " ['|TU0-13385|'],\n", + " ['|TU00223|'],\n", + " ['|TU0-14243|'],\n", + " ['|TU0-14168|']]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ecoli.all_operons()[0:10]" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 15, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|RXN-14142|',\n", + " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " '|2.7.10.1-RXN|',\n", + " '|5.99.1.2-RXN|',\n", + " '|1.5.1.34-RXN|',\n", + " '|RXN-17780|',\n", + " '|KETOACYLCOATHIOL-RXN|',\n", + " '|RXN0-7251|',\n", + " '|GLYCPDIESTER-RXN|',\n", + " '|LTAA-RXN|']" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "rxns\n", @@ -379,9 +553,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|DCYSDESULF-RXN|',\n", + " '|RXN-14142|',\n", + " '|RXN-12402|',\n", + " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " '|PUTTRANSAM-RXN|',\n", + " '|1.5.1.34-RXN|',\n", + " '|DHDOGALDOL-RXN|',\n", + " '|RXN-19777|',\n", + " '|RXN-12073|',\n", + " '|RXN-14285|']" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "rxns\n", @@ -389,15 +583,35 @@ "result of (all‑rxns :enzyme).\n", "\"\"\"\n", "\n", - "ecoli.rxns_catalyzed_by_complex(rxns = ecoli.all_rxns(':enzyme'))[0:10]\n", + "ecoli.rxns_catalyzed_by_complex(rxns = ecoli.all_rxns('enzyme'))[0:10]\n", "ecoli.rxns_catalyzed_by_complex()[0:10]" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|MHPELY-MONOMER|',\n", + " '|G6571-MONOMER|',\n", + " '|G7751-MONOMER|',\n", + " '|G7910-MONOMER|',\n", + " '|G6904-MONOMER|',\n", + " '|PGLUCONDEHYDRAT-MONOMER|',\n", + " '|MONOMER0-1241|',\n", + " '|ACECITLY-CPLX|',\n", + " '|G7422-MONOMER|',\n", + " '|EG12069-MONOMER|']" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "\"\"\"\n", "type\n", @@ -423,18 +637,38 @@ "\"\"\"\n", "\n", "ecoli.all_enzymes()[0:10]\n", - "ecoli.all_enzymes(type = ':any')[0:10]\n", - "ecoli.all_enzymes(type = ':chemical-change')[0:10]\n", - "ecoli.all_enzymes(type = ':small-molecule')[0:10]\n", - "ecoli.all_enzymes(type = ':transport')[0:10]\n", - "ecoli.all_enzymes(type = ':non-transport')[0:10]" + "ecoli.all_enzymes(type_of_reactions = ':any')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':small-molecule')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':transport')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':non-transport')[0:10]" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['|DCUA-MONOMER|',\n", + " '|G7399-MONOMER|',\n", + " '|YIDT-MONOMER|',\n", + " '|CORA-MONOMER|',\n", + " '|EG12134-MONOMER|',\n", + " '|EG11486-MONOMER|',\n", + " '|CYNX-MONOMER|',\n", + " '|YJDL-MONOMER|',\n", + " '|EG11512-MONOMER|',\n", + " '|GLTP-MONOMER|']" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ecoli.all_transporters()[0:10]" ] @@ -449,21 +683,21 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 2", + "display_name": "Python 3", "language": "python", - "name": "python2" + "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" + "pygments_lexer": "ipython3", + "version": "3.6.7" } }, "nbformat": 4, diff --git a/examples/Operations_on_Compounds.ipynb b/examples/Operations_on_Compounds.ipynb new file mode 100644 index 0000000..8de4802 --- /dev/null +++ b/examples/Operations_on_Compounds.ipynb @@ -0,0 +1,289 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "\n", + "compounds = [x.frameid for x in ecoli.compounds.instances][0:2]\n", + "reactions = [x.frameid for x in ecoli.reactions.instances][0:2]\n", + "enzymes = ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|RXN0-5298|'], ['|RXN0-1922|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "cpd\n", + "A child of class |Compounds|. \n", + "non-specific-too?\n", + "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", + "parent of cpd, appears as a substrate. \n", + "transport-only?\n", + "Keyword, Optional If non-nil, return only transport reactions. \n", + "compartment\n", + "Keyword, Optional If non-nil, return only reactions within the specified \n", + "compartment. \n", + "enzymatic?\n", + "Keyword, Optional If non-nil, return only enzymatic reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.reactions_of_compound(compound, enzymatic = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for compound in compounds:\n", + " for reaction in reactions:\n", + " lst.append(ecoli.substrate_of_generic_rxn(compound, reaction))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|FUCCAT-PWY|', '|FUC-RHAMCAT-PWY|'], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "cpd\n", + "An instance of class |Compounds|. \n", + "non-specific-too?\n", + "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", + "parent of cpd, appears as a substrate. \n", + "modulators?\n", + "Keyword, Optional If non-nil, returns pathways where cpd appears as a regulator \n", + "as well. \n", + "phys-relevant?\n", + "Keyword, Optional If true, then only return inhibitors that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "include-rxns?\n", + "Keyword, Optional If non-nil, then return a list of reaction-pathway pairs. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.pathways_of_compound(compound))#, modulators = True, include_rxns = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "\"\"\"\n", + "cpds\n", + "An instance or list of instances of class |Compounds|. \n", + "mode\n", + "Keyword, Optional Represents the type of regulation. Can take on the values of \n", + "“+”, “-”, or 'nil. \n", + "mechanisms\n", + "Keyword, Optional Keywords from the 'mechanism slot of the corresponding \n", + "sub-class of the class |Regulation|. If non-nil, only regulation objects with \n", + "mechanisms in this list will be explored for regulated objects. \n", + "phys-relevant?\n", + "Keyword, Optional If true, then only return inhibitors that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "slots\n", + "Keyword A list of enzymatic reaction slots to \n", + "\"\"\"\n", + "\n", + "try:\n", + " lst = []\n", + " for compound in compounds:\n", + " lst.append(ecoli.activated_or_inhibited_by_compound(compound))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for compound in compounds:\n", + " lst.append(ecoli.tfs_bound_to_compound(compound, include_inactive = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['dsbd-rxn', 'rxn0-4342']\n", + "['4-hydroxy-2-oxovalerate aldolase', 'L,D-transpeptidase YcfS']\n" + ] + } + ], + "source": [ + "# Object Name Manipulation Operations\n", + "# lst = []\n", + "# for reaction in reactions:\n", + "# lst.append(ecoli.get_name_string(reaction))\n", + "# print lst[-10:]\n", + "# print ''\n", + "\n", + "lst = []\n", + "for reaction in reactions:\n", + " lst.append(ecoli.full_enzyme_name(reaction))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for enzyme in enzymes:\n", + " lst.append(ecoli.enzyme_activity_name(enzyme))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Enzymatic-Reactions.ipynb b/examples/Operations_on_Enzymatic-Reactions.ipynb new file mode 100644 index 0000000..05be910 --- /dev/null +++ b/examples/Operations_on_Enzymatic-Reactions.ipynb @@ -0,0 +1,268 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " lst.append(ecoli.cofactors_and_pgroups_of_enzrxn(enzrxn = enzrxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "er\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "phys-relevant-only?\n", + "Optional If true, then only return activators that are associated with \n", + "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", + "non-nil. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_activators(enzrxn = enzrxn, phys_relevant_only=True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzrxn_inhibitors(enzrxn = enzrxn, phys_relevant_only = True))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "include-super-pwys?\n", + "Keyword, Optional If non-nil, then not only will the direct pathways in which \n", + "enzrxn is associated in be returned, but also any enclosing super-pathways. If \n", + "enzrxn is associated with a reaction that is directly associated with a \n", + "super-pathway, then the function might return super-pathways even if this option \n", + "is nil.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.pathways_of_enzrxn(enzrxn = enzrxn, include_super_pwys = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "enzrxn\n", + "An instance of the class |Enzymatic‑Reactions|. \n", + "single-species\n", + "Optional An instance of the class |Organisms| If set, then enzrxn has the \n", + "further stricture that it must be an enzymatic reaction present in the organism \n", + "specified by the value passed to single‑species.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " for rxn1 in ecoli.all_rxns(type_of_reactions = 'all'):\n", + " for rxn2 in ecoli.all_rxns(type_of_reactions = 'metab-smm'):\n", + " lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n", + " pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Genes.ipynb b/examples/Operations_on_Genes.ipynb new file mode 100644 index 0000000..1506a61 --- /dev/null +++ b/examples/Operations_on_Genes.ipynb @@ -0,0 +1,608 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "genes = [x.frameid for x in ecoli.genes.instances][0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|Genes|', '|Genes|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.gene_p(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.enzymes_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|EG11414-MONOMER|', '|CPLX0-7910|', '|CPLX0-3803|'], ['|EG11127-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.all_products_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.reactions_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.pathways_of_gene(gene, True, True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.chromosome_of_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|EG11414-MONOMER|', '|EG11127-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.unmodified_gene_product(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|EG11414-MONOMER|'], ['|EG11127-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.unmodified_gene_products(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|EG10850|', '|EG11024|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.next_gene_on_replicon(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|G7950|', '|EG11126|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.previous_gene_on_replicon(gene = gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "both queries are the same.\n", + "both queries are the same.\n", + "[None, False, False, None]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene1 in genes:\n", + " for gene2 in genes:\n", + " lst.append(ecoli.adjacent_genes_p(gene1, gene2))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "both queries are the same.\n", + "both queries are the same.\n", + "[None, False, False, None]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene1 in genes:\n", + " for gene2 in genes:\n", + " lst.append(ecoli.neighboring_genes_p(gene1, gene2))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'|EG11127|': ['|EG11414|']}" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.gene_clusters(genes, 4000)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for gene in genes:\n", + " lst.append(ecoli.rna_coding_gene(gene=gene))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for gene in genes:\n", + " lst.append(ecoli.protein_coding_gene(gene=gene))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.pseudo_gene_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.phantom_gene_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.dna_binding_site_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.terminator_p(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-36411|', '|TU0-13193|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.operon_of_gene(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|EG12115|', '|EG10850|', '|EG11414|'], ['|EG11125|', '|EG11126|', '|EG11127|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_in_same_operon(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.gene_transcription_units(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|EG12115|', '|EG10850|'], ['|EG11125|', '|EG11126|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.cotranscribed_genes(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.terminators_affecting_gene(gene=gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.chromosome_of_object(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Pathways.ipynb b/examples/Operations_on_Pathways.ipynb new file mode 100644 index 0000000..539ab4f --- /dev/null +++ b/examples/Operations_on_Pathways.ipynb @@ -0,0 +1,397 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|EG12082|',\n", + " '|EG12088|',\n", + " '|EG12090|',\n", + " '|EG12091|',\n", + " '|EG12092|',\n", + " '|EG11773|',\n", + " '|EG12093|',\n", + " '|EG12089|',\n", + " '|EG12087|',\n", + " '|EG11774|',\n", + " '|EG12086|',\n", + " '|EG12084|',\n", + " '|EG12083|',\n", + " '|EG10330|',\n", + " '|EG10331|',\n", + " '|EG10332|',\n", + " '|EG10333|']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "sorted?\n", + "Keyword, Optional If true, the genes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = 'all', base = True):\n", + " lst.append(ecoli.genes_of_pathway(pwy = pwy, sorted = True))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|NADH-DHI-CPLX|', '|FUMARATE-REDUCTASE|']" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "sorted?\n", + "Keyword, Optional If true, the enzymes are sorted in the order in which the \n", + "corresponding reaction occurrs in the sequence of the pathway. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.enzymes_of_pathway(pwy = pwy, sorted = True, experimental_only = True))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|FUM|',\n", + " '|SUC|',\n", + " '|Menaquinones|',\n", + " '|Menaquinols|',\n", + " '|E-|',\n", + " '|PROTON|',\n", + " '|NAD|',\n", + " '|NADH|']" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.compounds_of_pathway(pwy = pwy))\n", + "lst[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NADH|',\n", + " '|Menaquinones|',\n", + " '|Menaquinols|',\n", + " '|PROTON|',\n", + " '|TRIMETHYLAMINE-N-O|'],\n", + " ['|TRIMETHYLAMINE-N-O|', '|NADH|'],\n", + " ['|NAD|',\n", + " '|Menaquinols|',\n", + " '|PROTON|',\n", + " '|TRIMETHYLAMINE|',\n", + " '|WATER|',\n", + " '|Menaquinones|'],\n", + " ['|WATER|', '|TRIMETHYLAMINE|', '|NAD|']]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.substrates_of_pathway(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[],\n", + " ['|PWY-7195|', '|PWY-6556|'],\n", + " ['|PWY0-1597|'],\n", + " ['|RIBOSYN2-PWY|'],\n", + " ['|PWY0-1295|', '|PWY-6556|'],\n", + " [],\n", + " ['|PWY0-1584|', '|PWY0-1581|', '|PWY0-1573|', '|PWY0-1352|'],\n", + " [],\n", + " [],\n", + " []]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.variants_of_pathway(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[['|RXN0-5264|', '|RXN0-5388|']], 1, 2, 2]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "pwy\n", + "An instance of the class |Pathways|, which is not a super-pathway (i.e., does \n", + "not have any entries in its 'sub‑pathways slot). \n", + "rxn-list\n", + "Optional The list of reactions to use as the starting list of connected \n", + "component clusters. Defaults to (get‑slot‑values pwy 'reaction‑list).\n", + "\n", + "pred-list\n", + "Optional The list of reaction predecessors to iterate from in order to cluster \n", + "the reactions in rxn‑list. Defaults to (get‑slot‑values pwy 'predecessors).\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.pathway_components(pwy = pwy))\n", + "lst[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, True, False, True, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", + " lst.append(ecoli.noncontiguous_pathway_p(pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|DMKCYT-RXN|', '|RXN-15348|', False],\n", + " ['|DMKCYT-RXN|', '|LACTALDREDUCT-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|PFLDEACTIV-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|OHMETPYRKIN-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-7094|', False],\n", + " ['|DMKCYT-RXN|', '|TRIOSEPISOMERIZATION-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-7298|', False],\n", + " ['|DMKCYT-RXN|', '|RXN0-1137|', False],\n", + " ['|DMKCYT-RXN|', '|BADH-RXN|', False],\n", + " ['|DMKCYT-RXN|', '|DMKCYT-RXN|', False]]" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn1\n", + "An instance of the class |Reactions|. \n", + "rxn2\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for pwy in ecoli.all_pathways(selector = ':all', base = True)[0:10]:\n", + " for rxn1 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", + " for rxn2 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", + " lst.append([rxn1, rxn2, ecoli.rxns_adjacent_in_pwy_p(rxn1 = rxn1, rxn2 = rxn2, pwy = pwy)])\n", + "# lst.append(ecoli.rxns_adjacent_in_pwy_p(rxn1 = u'|RXN0-5264|', rxn2 = u'|RXN0-5388|', pwy = pwy))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb b/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb new file mode 100644 index 0000000..cbe4808 --- /dev/null +++ b/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb @@ -0,0 +1,943 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "complexes = ecoli.all_protein_complexes()[0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", + "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "coefficients?\n", + "Keyword, Optional If true, then the second return value of the function will be \n", + "a list of monomer coefficients. Defaults to true. \n", + "unmodify?\n", + "Keyword, Optional If true, obtain the monomers of the unmodified form of p.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein, coefficients = True, unmodify = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.monomers_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", + "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "exclude-small-molecules?\n", + "Keyword, Optional If nil, then small molecule components are also returned. \n", + "Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein, exclude_small_molecules = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.base_components_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.containers_of(protein = protein, exclude_self = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "exclude-self?\n", + "Optional If true, then protein will not be included in the return value. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, True]\n", + "[True, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|CPLX0-7660|', '|CPLX0-8247|']\n", + "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|CPLX0-7660|', '|CPLX0-8247|']\n", + "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "prots\n", + "A list of instances of the class |Proteins|. \n", + "debind?\n", + "Keyword, Optional When non-nil, the proteins are further simplified by obtaining \n", + "the unbound form of the protein, if it is bound to a small molecule. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein], debind = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reduce_modified_proteins(prots = [protein]))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_forms(protein = protein, all_variants = True, exclude_self= True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.modified_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", + "[['|CPLX0-3970|', '|ABC-22-CPLX|'], ['|CPLX0-7992|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.top_containers(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106|'], ['|EG12129|']]\n", + "[['|EG10676|'], ['|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6106|'], ['|EG12129|']]\n", + "[['|EG10676|'], ['|G7665|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_of_proteins(prots = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "protein\n", + "An instance of the class |Proteins|. \n", + "kb\n", + "Keyword, Optional The KB object of the KB in which to find the associated \n", + "reactions. Defaults to the current PGDB. \n", + "include-specific-forms?\n", + "Keyword, Optional When true, specific forms of associated generic reactions are \n", + "also returned. Default value is true. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein, include_subreactions = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_enzyme(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|ECOLI|'], ['|ECOLI|']]\n", + "[['|ECOLI|'], ['|ECOLI|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.species_of_protein(protein = protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, True]\n", + "[False, False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Optional Can take on one of the following values to select more precisely what \n", + "is meant by an “enzyme”:\n", + "\n", + ":any\n", + "Any protein that catalyzes a reaction is considered an enzyme. \n", + ":chemical-change\n", + "If the reactants and products of the catalyzed reactin differ, and not just by \n", + "their cellular location, then the protein is considered an enzyme. \n", + ":small-molecule\n", + "If the reactants of the catalyzed reaction differ and are small molecules, then \n", + "the protein is considered an enzyme. \n", + ":transport\n", + "If the protein catalyzes a transport reaction. \n", + ":non-transport\n", + "If the protein only catalyzes non-transport reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'any'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'non-transport-non-pathway'))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in complexes:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.leader_peptide_p(protein = protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|Proteins|', '|Proteins|']\n", + "['|Proteins|', '|Proteins|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|Protein-Complexes|', '|Protein-Complexes|']\n", + "[False, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.complex_p(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "p\n", + "An instance of the class |Proteins|. \n", + "check-protein-components?\n", + "Optional If true, check all components of this protein for catalyzed reactions. \n", + "Defaults to true. \n", + "check-protein-containers?\n", + "Optional If true, check the containers and modified forms of the protein for \n", + "catalyzed reactions. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_containers = True))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_components = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, False]\n", + "['|CCI-CYTOSOL-GN|', False]\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = 'CCO-CYTOSOL'))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = ['CCO-CYTOSOL', 'CCO-MEMBRANE']))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|MTR-MONOMER|', '|G7942-MONOMER|', '|NANT-MONOMER|', '|B1006-MONOMER|', '|YDHE-MONOMER|', '|YDEA-MONOMER|', '|PITA-MONOMER|', '|YEIM-MONOMER|', '|BCR-MONOMER|', '|YGFO-MONOMER|']\n" + ] + } + ], + "source": [ + "\"\"\"\n", + "membranes\n", + "Keyword Either :all or a list of instances of the class. Defaults to :all \n", + "'CCO‑MEMBRANE. \n", + "method\n", + "Either :location or :reaction‑compartments. :location will check the 'locations \n", + "slot, while :reaction‑compartments will examine the compartments of reaction \n", + "substrates. Default value is :location. \n", + "\"\"\"\n", + "\n", + "lst = ecoli.all_transporters_across(membranes = 'all')\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n", + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in complexes:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Reactions.ipynb b/examples/Operations_on_Reactions.ipynb new file mode 100644 index 0000000..a31329a --- /dev/null +++ b/examples/Operations_on_Reactions.ipynb @@ -0,0 +1,764 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|G6350|'],\n", + " ['|EG10754|'],\n", + " [],\n", + " [],\n", + " [],\n", + " ['|EG10068|'],\n", + " ['|EG10278|', '|G7213|'],\n", + " [],\n", + " ['|G7590|'],\n", + " []]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.genes_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NICOTINATE_NUCLEOTIDE|', '|ATP|', '|PROTON|', '|PPI|', '|DEAMIDO-NAD|'],\n", + " ['|ACETALD|', '|PYRUVATE|', '|PROTON|', '|ACETOIN|', '|CARBON-DIOXIDE|'],\n", + " ['|Protein-Red-Disulfides|',\n", + " '|MONOMER0-4152|',\n", + " '|MONOMER0-4438|',\n", + " '|Protein-Ox-Disulfides|'],\n", + " ['|PROTON|', '|AMINO-OXOBUT|', '|AMINO-ACETONE|', '|CARBON-DIOXIDE|'],\n", + " ['|Cytochromes-B-Reduced|', '|Cytochromes-B|', '|Reduced-Cytochromes-o|'],\n", + " ['|ATP|',\n", + " '|L-CITRULLINE|',\n", + " '|L-ASPARTATE|',\n", + " '|PROTON|',\n", + " '|L-ARGININO-SUCCINATE|',\n", + " '|PPI|',\n", + " '|AMP|'],\n", + " ['|ACETYL-COA|', '|CPD-7221|', '|CPD-15244|', '|CO-A|'],\n", + " ['|MONOMER0-1641|', '|TORR-CPLX|', '|CPLX0-2821|'],\n", + " ['|ATP|',\n", + " '|D-BETA-D-HEPTOSE-1-P|',\n", + " '|PROTON|',\n", + " '|ADP-D-GLYCERO-D-MANNO-HEPTOSE|',\n", + " '|PPI|'],\n", + " ['|DSBD-MONOMER|', '|CPLX0-8004|', '|DSBG-MONOMER|', '|DSBDOXI-MONOMER|']]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.substrates_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|NICONUCADENYLYLTRAN-MONOMER|'],\n", + " ['|PYRUVOXID-CPLX|'],\n", + " [],\n", + " [],\n", + " [],\n", + " ['|CPLX0-238|'],\n", + " ['|G7213-MONOMER|', '|FADA-CPLX|'],\n", + " [],\n", + " ['|CPLX0-3661|'],\n", + " []]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "species\n", + "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", + "MetaCyc, only proteins found in those organisms will be returned. This list can \n", + "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", + "the documentation for the 'species slot‑unit for more information. Default value \n", + "is nil. \n", + "experimental-only?\n", + "Keyword, Optional When true, only return enzymes that have a non-computational \n", + "evidence code associated with it. \n", + "local-only-p\n", + "Keyword, Optional When true, only return enzymes that catalyze the specific form \n", + "of the reaction, as opposed to enzymes that are known to catalyze a more general \n", + "form (i.e., class) of the reaction. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.enzymes_of_reaction(rxn = rxn, species = u'|ECOLI|', \n", + " experimental_only = False, local_only_p = False))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[['|PROTON|', '|ATP|', '|NICOTINATE_NUCLEOTIDE|'],\n", + " ['|PPI|', '|DEAMIDO-NAD|']],\n", + " [['|PROTON|', '|PYRUVATE|', '|ACETALD|'], ['|ACETOIN|', '|CARBON-DIOXIDE|']],\n", + " [['|MONOMER0-4152|', '|Protein-Red-Disulfides|'],\n", + " ['|MONOMER0-4438|', '|Protein-Ox-Disulfides|']],\n", + " [['|AMINO-OXOBUT|', '|PROTON|'], ['|AMINO-ACETONE|', '|CARBON-DIOXIDE|']],\n", + " [['|Cytochromes-B-Reduced|', '|Cytochromes-B|'],\n", + " ['|Cytochromes-B|', '|Reduced-Cytochromes-o|']],\n", + " [['|L-ASPARTATE|', '|L-CITRULLINE|', '|ATP|'],\n", + " ['|PROTON|', '|L-ARGININO-SUCCINATE|', '|PPI|', '|AMP|']],\n", + " [['|CPD-15244|', '|CO-A|'], ['|CPD-7221|', '|ACETYL-COA|']],\n", + " None,\n", + " [['|PROTON|', '|D-BETA-D-HEPTOSE-1-P|', '|ATP|'],\n", + " ['|ADP-D-GLYCERO-D-MANNO-HEPTOSE|', '|PPI|']],\n", + " None]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "direction\n", + "Keyword, Optional Can take on the following values:\n", + "\n", + ":L2R\n", + "The reaction direction goes from ‘left to right’, as described in the \n", + "|Reactions| instance. \n", + ":R2L\n", + "The reaction direction goes from ‘right to left’; the opposite of what is \n", + "described in the |Reactions| instance. \n", + "\n", + "pwy\n", + "Keyword, Optional An instance of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.reaction_reactants_and_products(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|SMALL-MOLECULE|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|',\n", + " '|SMALL-MOLECULE|',\n", + " '|PROTEIN-REACTION|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.reaction_type(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_without_sequenced_enzyme_p\u001b[0;34m(self, rxn)\u001b[0m\n\u001b[1;32m 1111\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1112\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1113\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1115\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "complete?\n", + "Optional If true, the predicate will return true when there is any associated \n", + "gene without a sequence. If nil, the predicate will return true when all \n", + "associated genes are without a sequence. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_without_sequenced_enzyme_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is REACTION-WITHOUT-SEQUENCED-ENZYME-P, \n", + "# which only argument is a rxn" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "hole-if-any-gene-without-position?\n", + "Keyword, Optional If true, then genes without specified coordinates for the \n", + "current organism’s genome are not counted when determining the status of the \n", + "reaction.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.pathway_hole_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1139\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1140\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1141\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1142\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1143\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." + ] + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_present_p(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is RXN-PRESENT?" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "specific-rxn\n", + "A child of the class |Reactions|. \n", + "generic-rxn\n", + "A child of the class |Reactions|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_specific_form_of_rxn_p(specific_rxn = rxn, generic_rxn = u'|RXN0-3741|'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.nonspecific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.specific_forms_of_rxn(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, False, False, False, False]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "compartments\n", + "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", + "See frame 'CCO. \n", + "default-ok?\n", + "Keyword, Optional If true, then we return true if the reaction has no associated \n", + "compartment information, or one of its associated locations is a super-class of \n", + "one of the members of the compartments argument. \n", + "pwy\n", + "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", + "rxn is limited to the given child of |Pathways|. \n", + "loose?\n", + "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", + "are treated as being the same compartment.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_in_compartment_p(rxn = rxn, compartments = [u'|CCO_CYTOSOL|']))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "ename": "PToolsError", + "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1240\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCell\u001b[0m \u001b[0mCompartment\u001b[0m \u001b[0mOntology\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1241\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1242\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1244\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" + ] + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "default\n", + "Optional The default compartment for reactions without any compartment \n", + "annotations on their substrates. The default value is 'CCO‑CYTOSOL. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.compartment_of_rxn(rxn = rxn))\n", + "lst[-10:]\n", + "\n", + "# this raise an error because the lisp function is missing (?)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-PERI-BAC|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-CYTOSOL|'],\n", + " ['|CCO-PERI-BAC|']]" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "sides\n", + "Keyword, Optional The slots of the reaction to consider. The default value is \n", + "'(LEFT RIGHT). \n", + "default-compartment\n", + "The default compartment, as determined by the function (default‑compartment), \n", + "which currently is set to 'CCO‑CYTOSOL.\n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.compartments_of_reaction(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|Nucleosides|'],\n", + " ['|D-ALANINE|', '|PROTON|'],\n", + " ['|GUANINE|'],\n", + " ['|DEOXYINOSINE|', '|PROTON|'],\n", + " ['|PROTON|', '|CPD0-2241|'],\n", + " ['|Inorganic-Compounds|'],\n", + " ['|PROTON|', '|D-GALACTURONATE|'],\n", + " ['|CPD0-2486|'],\n", + " ['|MELIBIOSE|', '|LI+|'],\n", + " ['|FORMATE|']]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "side\n", + "Keyword, Optional The side of the reaction from which to return the transported \n", + "compound. \n", + "primary-only?\n", + "Keyword, Optional If true, then filter out common exchangers (currently defined \n", + "as '(PROTON NA CPD-1)+). If true, and the only transported compounds are in this \n", + "list, then the filter doesn’t apply. \n", + "from-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported from that compartment. \n", + "to-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", + "return compounds transported to that compartment. \n", + "show-compartment\n", + "Keyword, Optional A compartment (child of class 'CCO). If specified, and the \n", + "compound is modified during transport, then only return the form of the compound \n", + "as found in this compartment. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':transport'):\n", + " lst.append(ecoli.transported_chemicals(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.get_predecessors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[[], [], [], [], [], [], [], [], [], []]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxn\n", + "An instance of the class |Reactions|. \n", + "pwy\n", + "A child of the class |Pathways|. \n", + "\"\"\"\n", + "\n", + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.get_successors(rxn = rxn, pwy = u'PWY0-1347'))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[False, False, False, False, False, False, True, False, False, False]" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lst = []\n", + "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", + " lst.append(ecoli.rxn_w_isozymes_p(rxn = rxn))\n", + "lst[-10:]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/Operations_on_Regulation_Frames.ipynb b/examples/Operations_on_Regulation_Frames.ipynb new file mode 100644 index 0000000..55f94a3 --- /dev/null +++ b/examples/Operations_on_Regulation_Frames.ipynb @@ -0,0 +1,1011 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", + "\n", + "regs = [x.frameid for x in ecoli.regulation.instances][0:2]\n", + "genes = [x.frameid for x in ecoli.genes.instances][0:2]\n", + "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", + "tus = [x.frameid for x in ecoli.transcription_units.instances][0:2]\n", + "dna_sites = [x.frameid for x in ecoli.DNA_Binding_Sites.instances][0:2]\n", + "mrna_sites = [x.frameid for x in ecoli.mRNA_Binding_Sites.instances][0:2]\n", + "terminators = [x.frameid for x in ecoli.Terminators.instances][0:2]\n", + "promoters = [x.frameid for x in ecoli.Promoters.instances][0:2]" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[True, False]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.activation_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[False, True]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.inhibition_p(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_activators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.direct_inhibitors(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_p(protein))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.regulator_of_type(protein, class_name = ':activator'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.regulon_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU162|'], ['|TU461|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for reg in regs:\n", + " lst.append(ecoli.regulation_frame_transcription_units(reg))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|REG0-11053|', '|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_regulation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activation_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|REG0-11053|', '|REG0-11052|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibition_frames(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_units_of_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.genes_regulated_by_protein(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.DNA_binding_sites_of_protein(protein, all_forms = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulator_proteins_of_transcription_unit(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " lst = []\n", + " for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_ligands(protein, u':both'))\n", + " print(lst[-10:])\n", + "except:\n", + " pass" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for protein in proteins:\n", + " lst.append(ecoli.transcription_factor_active_forms(protein))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|G6761|', '|EG10457|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulating_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.genes_regulated_by_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[None, None, None], [['|G6761-MONOMER|'], ['|PD00288|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.regulators_of_gene_transcription(gene, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_activators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_inhibitors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[None, None, None], [None, ['|PD01379|'], None]]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.regulators_of_operon_transcription(tu, by_function = True))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[None, '|PM0-8720|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_promoter(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6954|'], ['|EG11346|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_genes(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|G6954|', '|EG11346|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_first_gene(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|BS0-8048|', '|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|PD01379|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_transcription_factors(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_mrna_binding_sites(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.chromosome_of_operon(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], ['|BS0-7937|', '|BS0-7936|', '|BS0-7935|', '|BS0-7225|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_sites_affecting_gene(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for gene in genes:\n", + " lst.append(ecoli.binding_site_to_regulators(gene))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|PHOSPHO-PHOB|'], ['|CPLX0-7639|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_to_regulators(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-13975|'], ['|TU0-8636|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.transcription_units_of_promoter(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for promoter in promoters:\n", + " lst.append(ecoli.promoter_binding_sites(promoter))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[[], []]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_terminators(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-8814|'], ['|TU0-8340|']]\n", + "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n", + "[['|TU0-2021|'], ['|TU0-13514|']]\n", + "[['|TU0-13975|'], ['|TU0-8636|']]\n", + "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n", + "[['|TU-8390|', '|TU-8389|'], ['|TU00091|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_tus(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n", + "['|COLI-K12|', '|COLI-K12|']\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in mrna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in dna_sites:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in promoters:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in genes:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for tu in terminators:\n", + " lst.append(ecoli.containing_chromosome(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|PM0-2201|'], ['|PM0-9620|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_promoters(dna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|G6954|'], ['|PM0-8720|', '|EG11346|', '|BS0-8048|', '|BS0-8047|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for tu in tus:\n", + " lst.append(ecoli.transcription_unit_all_components(tu))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[['|TU0-2021|'], ['|TU0-13514|']]\n", + "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n" + ] + } + ], + "source": [ + "lst = []\n", + "for dna_site in dna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(dna_site))\n", + "print(lst[-10:])\n", + "\n", + "lst = []\n", + "for mrna_site in mrna_sites:\n", + " lst.append(ecoli.binding_site_transcription_units(mrna_site))\n", + "print(lst[-10:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/enumeration_operations.ipynb b/examples/enumeration_operations.ipynb new file mode 100644 index 0000000..95419ac --- /dev/null +++ b/examples/enumeration_operations.ipynb @@ -0,0 +1,705 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "#to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "import socket\n", + "hostname = socket.gethostname()\n", + "if hostname == \"spica\":\n", + " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", + "else:\n", + " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['',\n", + " '/usr/lib/python36.zip',\n", + " '/usr/lib/python3.6',\n", + " '/usr/lib/python3.6/lib-dynload',\n", + " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", + " '/usr/local/lib/python3.6/dist-packages',\n", + " '/usr/lib/python3/dist-packages',\n", + " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", + " '/home/glucksfall/.ipython',\n", + " '/opt/github-repositories/PythonCyc.networkbiolab']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", + "import os\n", + "import sys\n", + "if hostname == \"spica\":\n", + " path = '/opt/github-repositories'\n", + "else:\n", + " path = '/shared/D1/opt/github-repositories'\n", + "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", + "sys.path.append(module_path)\n", + "\n", + "sys.path" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|META|', '|ECOLI|']\n" + ] + } + ], + "source": [ + "import pythoncyc\n", + "all_orgids = pythoncyc.all_orgids()\n", + "print(all_orgids)\n", + "\n", + "meta = pythoncyc.select_organism(u'|META|')\n", + "ecoli = pythoncyc.select_organism(u'|ECOLI|')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|PWY0-1347|',\n", + " '|PWY-6690|',\n", + " '|PWY0-1348|',\n", + " '|PWY-5162|',\n", + " '|PWY0-1352|',\n", + " '|PWY0-1355|',\n", + " '|2PHENDEG-PWY|',\n", + " '|PWY0-1465|',\n", + " '|TRESYN-PWY|',\n", + " '|PANTO-PWY|']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "selector\n", + "Optional Selects whether all pathways, or just small-molecule metabolism base \n", + "pathways. Can take either a symbol of :all or :small‑molecule. Defaults to \n", + ":all. \n", + "base?\n", + "Optional If this argument evaluates to true, only includes base pathways. \n", + "Otherwise, all pathways, including superpathways, will be returned. \n", + "\"\"\"\n", + "\n", + "ecoli.all_pathways(selector = 'all', base = True)[0:10]\n", + "ecoli.all_pathways(selector = 'small-molecule', base = True)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|RXN-17635|',\n", + " '|RXN-6268|',\n", + " '|RXN-7282|',\n", + " '|RXN-10720|',\n", + " '|RXN-12870|',\n", + " '|RXN-14515|',\n", + " '|RXN-13460|',\n", + " '|RXN-14808|',\n", + " '|RXN-18819|',\n", + " '|RXN-15121|']" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Optional The type of reaction to return. Defaults to :metab‑smm. The possible \n", + "values are:\n", + "\n", + ":all\n", + "All reactions. \n", + ":metab-pathways\n", + "All reactions found within metabolic pathways. Includes reactions that are \n", + "pathway holes. May include a handfull of reactions whose substrates are \n", + "macromolecules, e.g., ACP. Excludes transport reactions. \n", + ":metab-smm\n", + "All reactions of small molecule metabolism, whether or not they are present in a \n", + "pathway. Subsumes :metab‑pathways. \n", + ":metab-all\n", + "All enzyme-catalyzed reactions. Subsumes :metab‑smm. \n", + ":enzyme\n", + "All enzyme-catalyzed reactions (i.e., instances of either EC-Reactions class or \n", + "Unclassified-Reactions class). \n", + ":transport\n", + "All transport reactions. \n", + ":small-molecule\n", + "All reactions whose substrates are all small molecules, as opposed to \n", + "macromolecules. Excludes transport reactions. \n", + ":protein-small-molecule-reaction\n", + "One of the substrates of the reaction is a macromolecule, and one of the \n", + "substrates of the reaction is a small molecule. \n", + ":protein-reaction\n", + "All substrates of the reaction are proteins. \n", + ":trna-reaction\n", + "One of the substrates of the reaction is a tRNA. \n", + ":spontaneous\n", + "Spontaneous reactions. \n", + ":non-spontaneous\n", + "Non-spontaneous reactions that are likely to be enzyme catalyzed. Some reactions \n", + "will be returned for type :non‑spontaneous that will not be returned by \n", + ":enzyme. \n", + "\"\"\"\n", + "\n", + "ecoli.all_rxns(type_of_reactions = 'all')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-pathways')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-smm')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'metab-all')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'transport')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'small-molecule')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'protein-small-molecule-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'protein-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'trna-reaction')[0:10]\n", + "ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['|RXN-17635|']\n" + ] + }, + { + "data": { + "text/plain": [ + "['|Protein-Arginine-Aminocarbinol|',\n", + " '|PROTON|',\n", + " '|Protein-Arginine-Imidazolidine|']" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "A list of reaction frames. \n", + "\"\"\"\n", + "print(ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])\n", + "ecoli.all_substrates(rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|DIPYRROMETHANE|',\n", + " '|GTP|',\n", + " '|UBIQUINONE-8|',\n", + " '|AMMONIUM|',\n", + " '|LYS|',\n", + " '|HEME_O|',\n", + " '|CPD-18260|',\n", + " '|PQQ|',\n", + " '|SIROHEME|',\n", + " '|Mo-molybdopterin-cofactor|']" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_cofactors()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|DEOXY-RIBOSE-1P|',\n", + " '|CPD0-1546|',\n", + " '|CPD0-1545|',\n", + " '|NACL|',\n", + " '|Gramicidins|',\n", + " '|CPD0-1633|',\n", + " '|G7642-MONOMER|',\n", + " '|CPD-9229|',\n", + " '|PENICILLIN|',\n", + " '|CPD0-2358|']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_modulators()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|LI+|',\n", + " '|MELIBIOSE|',\n", + " '|D-GALACTURONATE|',\n", + " '|PROTON|',\n", + " '|CPD0-2241|',\n", + " '|GUANINE|',\n", + " '|Nucleosides|',\n", + " '|CPD-20888|',\n", + " '|XANTHINE|',\n", + " '|N-ACETYL-D-MANNOSAMINE-6P|']" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "from-compartment\n", + "Keyword, Optional The compartment that the chemical is coming from (see Cellular \n", + "Component Ontology). \n", + "to-compartment\n", + "Keyword, Optional The compartment that the chemical is going to (see Cellular \n", + "Component Ontology). \n", + "show-compartment\n", + "Keyword, Optional Show the form of the compound as it is present in the \n", + "specified compartment (see Cellular Component Ontology), if the compound is \n", + "modified during transport. \n", + "primary-only?\n", + "Keyword, Optional If true, filter out common transport compounds, such as \n", + "protons and Na+. \n", + "\"\"\"\n", + "\n", + "ecoli.all_transported_chemicals()[0:10]\n", + "ecoli.all_transported_chemicals(primary_only = True)[0:10]\n", + "ecoli.all_transported_chemicals(from_compartment = u'|CCO-CYTOSOL|')[0:10]\n", + "ecoli.all_transported_chemicals(to_compartment = u'|CCO-CYTOSOL|')[0:10]\n", + "ecoli.all_transported_chemicals(show_compartment = 'cell')[0:10] # not valid argument" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|CPLX0-7660|',\n", + " '|CPLX0-8247|',\n", + " '|CPLX0-3102|',\n", + " '|ACETYL-COA-CARBOXYLTRANSFER-CPLX|',\n", + " '|CPLX0-7|',\n", + " '|TRANS-CPLX-204|',\n", + " '|FLAGELLAR-MOTOR-COMPLEX|',\n", + " '|1-PFK|',\n", + " '|CPLX0-8125|',\n", + " '|CPLX0-7687|']" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "filter\n", + "Keyword The type of protein complexes to return. The argument must be one of the \n", + "following values:\n", + "\n", + ":all or t\n", + "Return all protein complexes. \n", + ":hetero\n", + "Return all heteromultimers. \n", + ":homo\n", + "Return all homomultimers. \n", + "\"\"\"\n", + "\n", + "ecoli.all_protein_complexes(filter = 'all')[0:10]\n", + "ecoli.all_protein_complexes(filter = 'hetero')[0:10]\n", + "ecoli.all_protein_complexes(filter = 'homo')[0:10]\n", + "ecoli.all_protein_complexes()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|G6165-MONOMER|',\n", + " '|PHOSPHO-NARP|',\n", + " '|G6882-MONOMER|',\n", + " '|MONOMER0-1|',\n", + " '|G7947-MONOMER|',\n", + " '|G6175-MONOMER|',\n", + " '|EG11554-MONOMER|',\n", + " '|PD01196|',\n", + " '|EG10087-MONOMER|',\n", + " '|EG10226-MONOMER|']" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "Side-Effects\n", + "\n", + "allow-modified-forms?\n", + "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", + "protein are returned. If false, then only unmodified forms of the proteins are \n", + "returned. The default value is t.\n", + "\"\"\"\n", + "\n", + "ecoli.all_transcription_factors()[0:10]\n", + "ecoli.all_transcription_factors(allow_modified_forms = True)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|G6165-MONOMER|',\n", + " '|NARP-MONOMER|',\n", + " '|TAR-CPLX|',\n", + " '|G6882-MONOMER|',\n", + " '|EG11140-MONOMER|',\n", + " '|EG10881-MONOMER|',\n", + " '|G7947-MONOMER|',\n", + " '|G6175-MONOMER|',\n", + " '|EG12111-MONOMER|',\n", + " '|EG11554-MONOMER|']" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "class\n", + "Keyword, Optional The class |Regulation| or a subclass. It defaults to \n", + "|Regulation‑of‑Transcription‑Initiation|. \n", + "allow-modified forms?\n", + "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", + "protein are returned. If false, then only unmodified forms of the proteins are \n", + "returned. The default value is t.\n", + "\"\"\"\n", + "\n", + "ecoli.all_genetic_regulation_proteins(class_name = u'|Regulation|', allow_modified_forms = False)[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|EG11355-MONOMER|',\n", + " '|RPOE-MONOMER|',\n", + " '|RPOD-MONOMER|',\n", + " '|RPON-MONOMER|',\n", + " '|PD00440|',\n", + " '|RPOS-MONOMER|',\n", + " '|RPOH-MONOMER|']" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_sigma_factors()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[['|TU0-8814|'],\n", + " ['|TU0-8710|'],\n", + " ['|TU0-13847|'],\n", + " ['|TU0-13769|'],\n", + " ['|TU0-13667|'],\n", + " ['|TU00321|'],\n", + " ['|TU0-13385|'],\n", + " ['|TU00223|'],\n", + " ['|TU0-14243|'],\n", + " ['|TU0-14168|']]" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_operons()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|RXN-14142|',\n", + " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " '|2.7.10.1-RXN|',\n", + " '|5.99.1.2-RXN|',\n", + " '|1.5.1.34-RXN|',\n", + " '|RXN-17780|',\n", + " '|KETOACYLCOATHIOL-RXN|',\n", + " '|RXN0-7251|',\n", + " '|GLYCPDIESTER-RXN|',\n", + " '|LTAA-RXN|']" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", + "result of (all‑rxns :enzyme).\n", + "\"\"\"\n", + "\n", + "ecoli.rxns_w_isozymes(rxns = ecoli.all_rxns(':enzyme'))[0:10]\n", + "ecoli.rxns_w_isozymes()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|DCYSDESULF-RXN|',\n", + " '|RXN-14142|',\n", + " '|RXN-12402|',\n", + " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", + " '|PUTTRANSAM-RXN|',\n", + " '|1.5.1.34-RXN|',\n", + " '|DHDOGALDOL-RXN|',\n", + " '|RXN-19777|',\n", + " '|RXN-12073|',\n", + " '|RXN-14285|']" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "rxns\n", + "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", + "result of (all‑rxns :enzyme).\n", + "\"\"\"\n", + "\n", + "ecoli.rxns_catalyzed_by_complex(rxns = ecoli.all_rxns('enzyme'))[0:10]\n", + "ecoli.rxns_catalyzed_by_complex()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|MHPELY-MONOMER|',\n", + " '|G6571-MONOMER|',\n", + " '|G7751-MONOMER|',\n", + " '|G7910-MONOMER|',\n", + " '|G6904-MONOMER|',\n", + " '|PGLUCONDEHYDRAT-MONOMER|',\n", + " '|MONOMER0-1241|',\n", + " '|ACECITLY-CPLX|',\n", + " '|G7422-MONOMER|',\n", + " '|EG12069-MONOMER|']" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\"\"\"\n", + "type\n", + "Keyword, Optional A type as taken from the argument to #'enzyme?. Defaults to \n", + ":chemical‑change.\n", + "\n", + ">> type\n", + "Optional Can take on one of the following values to select more precisely what \n", + "is meant by an “enzyme”:\n", + "\n", + ":any\n", + "Any protein that catalyzes a reaction is considered an enzyme. \n", + ":chemical-change\n", + "If the reactants and products of the catalyzed reactin differ, and not just by \n", + "their cellular location, then the protein is considered an enzyme. \n", + ":small-molecule\n", + "If the reactants of the catalyzed reaction differ and are small molecules, then \n", + "the protein is considered an enzyme. \n", + ":transport\n", + "If the protein catalyzes a transport reaction. \n", + ":non-transport\n", + "If the protein only catalyzes non-transport reactions. \n", + "\"\"\"\n", + "\n", + "ecoli.all_enzymes()[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':any')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':small-molecule')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':transport')[0:10]\n", + "ecoli.all_enzymes(type_of_reactions = ':non-transport')[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['|DCUA-MONOMER|',\n", + " '|G7399-MONOMER|',\n", + " '|YIDT-MONOMER|',\n", + " '|CORA-MONOMER|',\n", + " '|EG12134-MONOMER|',\n", + " '|EG11486-MONOMER|',\n", + " '|CYNX-MONOMER|',\n", + " '|YJDL-MONOMER|',\n", + " '|EG11512-MONOMER|',\n", + " '|GLTP-MONOMER|']" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ecoli.all_transporters()[0:10]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ptools API - Operations on Enzymatic-Reactions.ipynb b/examples/ptools API - Operations on Enzymatic-Reactions.ipynb deleted file mode 100644 index e011b10..0000000 --- a/examples/ptools API - Operations on Enzymatic-Reactions.ipynb +++ /dev/null @@ -1,34762 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import os\n", - "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", - "\n", - "sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", - "[u'|META|', u'|ECOLI|']\n" - ] - } - ], - "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns :all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns :all ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15348| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LACTALDREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PFLDEACTIV-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHMETPYRKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7094| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7298| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1137| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BADH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMKCYT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5061| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FES-OX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16000| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6505| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPCARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2601| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MENCYT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7003| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARNDETRU-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14505| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADPREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5118| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTAPD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16650| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEPHOSICITDEHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXNMETA-12672| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTEIN-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5183| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYL-KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10658| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16910| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16910| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12473| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12473| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2942| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2942| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|YIAE2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|YIAE2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUFLAVREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16330| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16330| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6359| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6359| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10661| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10661| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5245| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5245| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17935| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17935| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-385| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-385| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14107| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14107| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6490| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6490| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10851| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10851| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17014| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17014| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17661| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17661| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10981| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10981| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15140| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15140| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17474| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17474| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5254| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5254| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FMNREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FMNREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19445| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19445| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6954| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6954| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6462| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6462| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NICOTINAMID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICOTINAMID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8629| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8629| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17757| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17757| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.127-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.127-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9537| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9537| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5259| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5259| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18435| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18435| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THRESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THRESYN-RXN| ))\n", - 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"text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.11.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.11.2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9789| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9789| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16333| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16333| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-5822| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5822| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CATAL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CATAL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2145| )\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5501| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LCYSDESULF-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LCYSDESULF-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CITTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7309| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7309| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5294| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5294| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FMN-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FMN-RED-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R134-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R134-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACONITATEHYDR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATEHYDR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MCPTAP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTAP-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-261| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-261| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2605| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2605| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17724| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17724| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOBR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOBR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-293| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-293| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14510| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14510| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10654| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10654| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4741| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4741| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-NADP+-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-NADP+-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRIDOXKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIDOXKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11482| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11482| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|S-FORMYLGLUTATHIONE-HYDROLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|S-FORMYLGLUTATHIONE-HYDROLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17023| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17023| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6434| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6434| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENYLOSUCCINATE-SYNTHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLOSUCCINATE-SYNTHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMDECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMDECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18584| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18584| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7159| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7159| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2945| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2945| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19949| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19949| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R138-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R138-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14712| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14712| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5390| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5390| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9527| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9527| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2701| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2701| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHGLYSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHGLYSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9655| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9655| ))\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-GUANINE-N7--METHYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18678| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18678| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6707| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6707| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BASS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BASS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17936| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17936| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-20000| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-291| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-291| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CREC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CREC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.13.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.13.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4721| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4721| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5186| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5186| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18549| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18549| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARCA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5372| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5372| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16992| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16992| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHEBTRGD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTRGD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6409| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6409| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PNP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNP-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11578| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11578| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-ACP-REDUCT-NADH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7071| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7071| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DALADALALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DALADALALIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GSADENYLATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSADENYLATION-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R137-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R137-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5222| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5222| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GALACTURIDYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTURIDYLYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NARLQ-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARLQ-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-269| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-269| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17489| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17489| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYFLAVOXRE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYFLAVOXRE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-295| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-295| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6515| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6515| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10660| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10660| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5230| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5230| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEOXYINOPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYINOPHOSPHOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13039| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13039| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5389| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5389| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5297| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5297| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1TRANSKETO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1TRANSKETO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17013| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17013| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6466| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6466| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17726| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17726| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17363| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17363| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7171| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7171| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRIMSYN3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIMSYN3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19024| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19024| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19366| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19366| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R140-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R140-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIAMTRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMTRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7716| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7716| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-278| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-278| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5393| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5393| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11776| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11776| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9536| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9536| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17786| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17786| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9662| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9662| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5250| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5250| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R524-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R524-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUC1PURIDYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUC1PURIDYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-20| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-20| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5450| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5450| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DNA-CYTOSINE-5--METHYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-CYTOSINE-5--METHYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5194| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5194| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7271| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7271| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCGLUDESUCC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCGLUDESUCC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALKAPHOSPHA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALKAPHOSPHA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7239| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7239| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.3.1.179-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.179-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACP-S-ACETYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACP-S-ACETYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15041| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15041| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETOACETYL-COA-TRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOACETYL-COA-TRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHEBDEAMID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBDEAMID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROGENASE-QUINONE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADH-DEHYDROGENASE-QUINONE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYT-ACC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYT-ACC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THI-P-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THI-P-KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2044| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2044| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GCVP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GCVP-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MCPTRG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTRG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3962| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3962| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14409| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14409| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSICITDEHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15293| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15293| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10656| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10656| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIP-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIP-KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LEUCINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LEUCINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15891| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15891| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THYMIDYLATESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYMIDYLATESYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17127| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17127| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPARAGINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARAGINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-742| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-742| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18605| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18605| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4841| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4841| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19952| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19952| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15607| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15607| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACSERLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACSERLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9531| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9531| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OXALODECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALODECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9658| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9658| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRNA-S-TRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-S-TRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2606| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2606| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1140| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1140| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BETA-PHOSPHOGLUCOMUTASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETA-PHOSPHOGLUCOMUTASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4942| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4942| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5065| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5065| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14511| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14511| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6385| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6385| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-1623| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-1623| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6533| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6533| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGLUCISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLUCISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALIC-NADP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALIC-NADP-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7105| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7105| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPMANACATRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPMANACATRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7303| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7303| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SAICARSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SAICARSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-583| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-583| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5125| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5125| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.3.1.49-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.49-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16687| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16687| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENYLYLSULFKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLYLSULFKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALTARCA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTARCA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSACETYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSACETYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHEBTARD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEBTARD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|URPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-299| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-299| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DISULFOXRED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DISULFOXRED-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYCPHOSDIESTER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYCPHOSDIESTER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTAREDOXIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAREDOXIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5190| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5190| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14747| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14747| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MYRPALMTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MYRPALMTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16997| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16997| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROTEIN-TYROSINE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTEIN-TYROSINE-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|POLYPHOSPHATE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|POLYPHOSPHATE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHIONINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHIONINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10659| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10659| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DARABALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABALDOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17012| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17012| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5225| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5225| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCDIAMINOPIMDESUCC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCDIAMINOPIMDESUCC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17362| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17362| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17495| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17495| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19342| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19342| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRPPAMIDOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRPPAMIDOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALDOSE-1-EPIMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALDOSE-1-EPIMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7101| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7101| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEOXYRIBOSE-P-ALD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYRIBOSE-P-ALD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9535| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9535| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5305| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5305| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3364| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3364| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9661| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9661| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17753| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17753| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1147| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1147| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14992| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14992| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5177| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5177| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDRODIPICSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDRODIPICSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6442| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6442| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5402| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5402| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-GLN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-GLN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6560| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6560| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17789| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17789| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7169| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7169| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RHAMNISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RHAMNISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TETHYDPICSUCC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TETHYDPICSUCC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-746| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-746| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DNA-LIGASE-NAD+-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-LIGASE-NAD+-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMACYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMACYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5509| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5509| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMP-DEPHOSPHORYLATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMP-DEPHOSPHORYLATION-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.7.2.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.7.2.2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17887| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17887| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.7.61-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.61-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RNTRACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RNTRACTIV-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3922| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3922| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ATOC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATOC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ENTF-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTF-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15216| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15216| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOLO-ACP-SYNTH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOLO-ACP-SYNTH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18031| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18031| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NARPQ-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARPQ-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11319| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11319| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NMNNUCLEOSID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NMNNUCLEOSID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RCSC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RCSC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FUC4NACTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUC4NACTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11361| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11361| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6483| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6483| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THYM-PHOSPH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYM-PHOSPH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.274-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.274-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17015| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17015| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18707| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18707| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPAMINOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPAMINOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17823| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17823| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11592| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11592| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8655| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8655| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GARTRANSFORMYL2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GARTRANSFORMYL2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4621| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4621| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9539| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9539| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6524| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6524| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9787| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9787| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15578| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15578| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2142| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2142| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19256| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19256| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5211| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5211| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11834| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11834| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OROTPDECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OROTPDECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7196| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7196| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCONOLACT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCONOLACT-RXN| ))\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12445| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12445| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PEPTIDYLPROLYL-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPTIDYLPROLYL-ISOMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11477| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11477| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCOLALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLALDREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14499| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14499| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6977| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6977| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPGLUCEPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPGLUCEPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17018| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17018| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.21.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19617| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19617| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-6423| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6423| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9516| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9516| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12862| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12862| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9555| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9555| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GPPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GPPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5123| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5123| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9790| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9790| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7000| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7000| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-267| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-267| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.2.1.52-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.1.52-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16665| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16665| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5419| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5419| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8315| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8315| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6495| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6495| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13329| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13329| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOQ-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOQ-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-722| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-722| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-949| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-949| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7040| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7040| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UROGENIIISYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UROGENIIISYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.8.4.8-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.8.4.8-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.105-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.105-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.3.16-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.3.16-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8899| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8899| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CROBETREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CROBETREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.2.1.58-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.1.58-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14047| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14047| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CITC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5187| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5187| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FLAVONADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FLAVONADPREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7101| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7101| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALONYL-COA-ACP-TRANSACYL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALONYL-COA-ACP-TRANSACYL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4-NITROPHENYLPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4-NITROPHENYLPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16995| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16995| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PALMITOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PALMITOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9983| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9983| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RSTB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RSTB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14143| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14143| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PNPOXI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNPOXI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11480| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11480| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|INOSINEKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINEKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15511| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15511| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7168| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7168| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DAPASYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DAPASYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17021| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17021| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5.99.1.3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.99.1.3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17943| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17943| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1842| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1842| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5223| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5223| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19774| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19774| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14286| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14286| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9523| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9523| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KETOBUTFORMLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOBUTFORMLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17490| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17490| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9558| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9558| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7253| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7253| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1133| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1133| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROTOHEMEFERROCHELAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTOHEMEFERROCHELAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-307| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-307| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2201| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2201| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5514| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5514| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14479| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14479| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEOXYNUCLEOTIDE-3-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYNUCLEOTIDE-3-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6503| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6503| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LTARTDEHYDRA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LTARTDEHYDRA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7047| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7047| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-962| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-962| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5298| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5298| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7268| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7268| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADCLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADCLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-REDUCT-NADPH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOREDOXIN-REDUCT-NADPH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-268| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-268| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17745| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17745| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.3.1.128-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.128-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14521| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14521| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-22-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-22-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNITOL-1-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNITOL-1-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRNUTRANSHYDROGEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRNUTRANSHYDROGEN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SERINE-O-ACETTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SERINE-O-ACETTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CREB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CREB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AICARTRANSFORM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AICARTRANSFORM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIENOYLCOAREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIENOYLCOAREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GAMMA-GLUTAMYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GAMMA-GLUTAMYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-304| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-304| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MCPTAR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MCPTAR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14809| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14809| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5395| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5395| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10655| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10655| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-MUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-MUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11483| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11483| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCORNTRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCORNTRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17787| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17787| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15890| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15890| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALLOSE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLOSE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17024| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17024| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3543| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3543| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R621-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R621-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18604| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18604| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15122| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15122| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19950| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19950| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NAG1P-URIDYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAG1P-URIDYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-DNA-POLYMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-DNA-POLYMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9528| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9528| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9657| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9657| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARABISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARABISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5462| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5462| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1139| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1139| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4181| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4181| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3341| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3341| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15298| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15298| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17848| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17848| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7299| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7299| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|O-SUCCHOMOSERLYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|O-SUCCHOMOSERLYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-582| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-582| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-623| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-623| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBULPEPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBULPEPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.3.1.41-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.41-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-549| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-549| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5021| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5021| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-HYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENOYL-COA-HYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-569| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-569| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15761| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15761| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-588| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-588| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSDECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSDECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6371| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6371| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-609| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-609| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERILEU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERILEU-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17955| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17955| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-117| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-117| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5100| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5100| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-137| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-137| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16312| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16312| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17961| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17961| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-226| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-226| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLMURAMATEDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLMURAMATEDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11277| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11277| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5264| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5264| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHORISMATEMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORISMATEMUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-273| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-273| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5129| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5129| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FPPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FPPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRUVDEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUVDEH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16690| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16690| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-295| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-295| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSNACMURPENTATRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSNACMURPENTATRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6481| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6481| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-328| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-328| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|VALINE-PYRUVATE-AMINOTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|VALINE-PYRUVATE-AMINOTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-35| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-35| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYSTEINE-AMINOTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTEINE-AMINOTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.264-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.264-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-366| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-366| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5199| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5199| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-58| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-58| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17009| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17009| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18702| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18702| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PPGPPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPGPPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12588| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12588| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DCDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11589| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11589| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-209| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-209| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5228| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5228| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12894| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12894| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17631| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17631| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GAPOXNPHOSPHN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GAPOXNPHOSPHN-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-258| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-258| ))\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19629| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19629| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-591| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-591| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11397| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11397| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-612| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-612| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FUCULOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUCULOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11867| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18710| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18710| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-162| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-162| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11598| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11598| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6726| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6726| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-237| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-237| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5269| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5269| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6527| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6527| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2PGADEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2PGADEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-279| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-279| ))\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14073| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-703| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-703| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-616| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-616| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6485| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6485| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOMSUCTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMSUCTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108D| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108D| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7104| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7104| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.19.12-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.19.12-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.39-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.39-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.2.99.18-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.99.18-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-144| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-144| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1241| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1241| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8675| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8675| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CITLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18709| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18709| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14181| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14181| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ISOCHORSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCHORSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14025| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14025| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-241| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-241| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11596| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11596| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7187| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7187| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-282| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-282| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|6PGLUCONOLACT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6PGLUCONOLACT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSMET-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSMET-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-3| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-3| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDP-GLUCOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDP-GLUCOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1863| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1863| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-338| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-338| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14361| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14361| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7092| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7092| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-355| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-355| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6526| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6526| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|L-GLN-FRUCT-6-P-AMINOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-GLN-FRUCT-6-P-AMINOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-376| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-376| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7275| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7275| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3PGAREARR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3PGAREARR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-71| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-71| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETYLGLUTKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLGLUTKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-162| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-162| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2361| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2361| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9951| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9951| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-224| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-224| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19312| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19312| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14483| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14483| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13158| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13158| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LYSDECARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSDECARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14139| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14139| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-269| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-269| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11836| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11836| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-985| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-985| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-288| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-288| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENODEAMIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENODEAMIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|INOSINATE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINATE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-0| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-0| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2787| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2787| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.6.3.23-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.23-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14524| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14524| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7166| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7166| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6566| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6566| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNONOXIDOREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNONOXIDOREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-480| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-480| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SIROHEME-FERROCHELAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SIROHEME-FERROCHELAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5.4.2.10-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.4.2.10-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7210| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7210| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.1.148-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.1.148-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALADEHYDCHLORO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALADEHYDCHLORO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-16-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-16-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-310| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-310| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1603| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1603| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-500| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-500| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19776| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19776| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14812| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14812| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7244| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7244| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MHPELY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPELY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14284| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14284| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-36-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-36-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12072| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12072| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SULFATE-ADENYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFATE-ADENYLYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-518| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-518| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALTRO-OXIDOREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTRO-OXIDOREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KDUD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDUD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2561| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2561| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTKIN-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-363| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-363| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-539| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-539| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15125| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15125| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7250| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7250| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-561| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-561| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6733| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6733| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NANK-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NANK-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THREDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETOLACTSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOLACTSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-578| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-578| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-SYNTHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-SYNTHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARGDECARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGDECARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-600| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-600| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4261| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4261| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2101| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2101| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-1| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-1| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-2961| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2961| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15313| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15313| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108G| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108G| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14477| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14477| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12480| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12480| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRE6PHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRE6PHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5202| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5202| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPDECARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPDECARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LIPIDXSYNTHESIS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LIPIDXSYNTHESIS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-181A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-181A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCOPHOSPHORYL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOPHOSPHORYL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5040| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5040| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-25| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-25| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15889| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15889| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-901| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-901| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-285| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-285| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6979| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6979| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PANTEPADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTEPADENYLYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5388| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5388| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TYROSINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TYROSINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACYLCOASYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLCOASYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-31| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-31| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.21.7-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.7-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BTUR2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BTUR2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-341| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-341| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5107| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5107| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2625| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2625| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-359| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-359| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7253| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7253| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16456| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16456| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-379| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-379| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UNDECAPRENYL-DIPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UNDECAPRENYL-DIPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14514| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14514| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-77| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-77| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12869| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12869| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CITSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-201| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-201| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5144| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5144| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALTODEG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALTODEG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTAMATESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMATESYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GSDEADENYLATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSDEADENYLATION-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16765| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16765| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-228| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-228| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHASERSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHASERSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SELENOCYSTEINE-LYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SELENOCYSTEINE-LYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-273| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-273| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7002| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7002| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|XYLISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-444| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-444| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYTIDEAM2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDEAM2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AGMATIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AGMATIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7124| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7124| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.2.2.21-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.2.21-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5209| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5209| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-11| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-11| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17307| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17307| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-302| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-302| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-464| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-464| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8342| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8342| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7190| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7190| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DCUS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCUS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14807| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14807| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1684| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1684| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13459| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13459| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5240| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5240| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-487| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-487| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17634| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17634| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHYLISOCITRATE-LYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLISOCITRATE-LYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7217| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7217| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|H2PTERIDINEPYROPHOSPHOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2PTERIDINEPYROPHOSPHOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PTAALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PTAALT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DHBDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHBDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-503| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-503| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-705| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-705| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5363| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5363| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7247| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7247| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17779| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17779| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALLANTOATE-DEIMINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLANTOATE-DEIMINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-42-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-42-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.53-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.53-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|QUINOLINATE-SYNTHA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QUINOLINATE-SYNTHA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-522| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-522| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDROXYISOVALDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROXYISOVALDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3521| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3521| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-544| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-544| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8991| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8991| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5414| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5414| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-564| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-564| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17795| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17795| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15119| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15119| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-584| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-584| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14065| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14065| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNDEAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNDEAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-604| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-604| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DTDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NADPH-DEHYDROGENASE-FLAVIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADPH-DEHYDROGENASE-FLAVIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-101| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-129| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-129| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7103| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7103| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10639| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10639| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|F16ALDOLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|F16ALDOLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMYLOMALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMYLOMALT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-205A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-205A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.2.1.99-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.2.1.99-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6446| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6446| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-262| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-262| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6452| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6452| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4022| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4022| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-290| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-290| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1081| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1081| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18258| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18258| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R601-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R601-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11475| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11475| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15296| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15296| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-313| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-313| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14161| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14161| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GALACTARDEHYDRA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTARDEHYDRA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6502| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6502| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOSIDE-DIPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-346| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-346| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ISOCHORMAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCHORMAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.2.99.7-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.2.99.7-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-362| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-362| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18739| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18739| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-42| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-42| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7173| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7173| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11602| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11602| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-82| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-82| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDPPYPHOSKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPPYPHOSKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPARTASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-204| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-204| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|6PFRUCTPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6PFRUCTPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6531| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6531| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-236| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-236| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.1.1.72-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.72-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4961| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4961| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-276| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-276| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1862| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1862| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19343| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19343| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-447| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-447| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11840| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11840| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15743| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15743| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-467| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-467| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14325| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14325| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCUROISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCUROISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7200| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7200| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6677| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6677| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OXALYL-COA-DECARBOXYLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALYL-COA-DECARBOXYLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1702| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1702| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|L-ASPARTATE-OXID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-ASPARTATE-OXID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.7.13-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.13-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-492| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-492| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19919| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19919| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRNA-URACIL-5--METHYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-URACIL-5--METHYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7222| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7222| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7272| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7272| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12107| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12107| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-24-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-24-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLY3KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLY3KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BETAGALACTOSID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETAGALACTOSID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-507| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-507| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETYLESTERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLESTERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6944| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6944| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-63-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-63-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-NUCLEOTID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-NUCLEOTID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5073| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5073| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-525| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-525| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2301| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2301| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-3523| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3523| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-547| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-547| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12541| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12541| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16281| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16281| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-568| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-568| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14481| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14481| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOXI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-587| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-587| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6983| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6983| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGLUCONDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLUCONDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-608| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-608| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LXULRU5P-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LXULRU5P-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.26.3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7609| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7609| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPMANNACADEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPMANNACADEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-116| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-116| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-984| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-984| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12876| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12876| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-132| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-132| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-I-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-I-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHEYDEPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHEYDEPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-158| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENINE-DEAMINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENINE-DEAMINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7012| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7012| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-22| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-22| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.11.4-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.4-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5126| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5126| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5260| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5260| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-275| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-275| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17755| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17755| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-1381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-1381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16688| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16688| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-272| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-272| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14523| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14523| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HEMN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HEMN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5309| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5309| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7074| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7074| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSGLYPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSGLYPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-294| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-294| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNONDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNONDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.92-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.92-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-325| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-325| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9087| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9087| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|URUR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URUR-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-349| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-349| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14091| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14091| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11193| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11193| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HYPOTAURINE-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYPOTAURINE-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYSTATHIONINE-BETA-LYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTATHIONINE-BETA-LYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-365| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-365| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AKBLIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AKBLIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7119| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7119| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6554| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6554| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4OHBENZOATE-OCTAPRENYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4OHBENZOATE-OCTAPRENYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5192| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5192| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-57| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-57| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-308| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-308| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1342| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1342| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-92| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-92| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14249| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14249| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16998| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16998| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-207| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-207| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14811| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14811| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ISPH2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISPH2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12893| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12893| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7227| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7227| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PORPHOBILSYNTH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PORPHOBILSYNTH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-244| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-244| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MHPCHYDROL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPCHYDROL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACECOATRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACECOATRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7041| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7041| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1941| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1941| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DARABISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-279| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-279| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUGAR-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUGAR-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-451| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-451| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|L-RHAMNONATE-DEHYDRATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-RHAMNONATE-DEHYDRATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5226| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5226| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-470| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-470| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALPHAGALACTOSID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALPHAGALACTOSID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7285| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7285| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7203| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7203| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACID-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACID-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17629| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17629| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-18| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-18| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-361| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-361| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2441| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2441| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-27-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-27-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14501| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14501| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRPPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRPPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-510| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-510| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15124| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15124| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LYXISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYXISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2421| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2421| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN66-526| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN66-526| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEPHOSPHOCOAKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEPHOSPHOCOAKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-70-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-70-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NANE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NANE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENPHOSPHOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-528| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-528| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2921| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2921| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5306| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5306| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-551| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-551| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIOSULFATE-SULFURTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOSULFATE-SULFURTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14552| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14552| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-571| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-571| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNPISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNPISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17754| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17754| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15314| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15314| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARCBTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCBTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SPERMACTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SPERMACTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-590| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-590| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALARACECAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALARACECAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRROLINECARBREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4522| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4522| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4223| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4223| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3201| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3201| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-611| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-611| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14850| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14850| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATEREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROFOLATEREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15312| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15312| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUCOSAMINE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUCOSAMINE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASNSYNB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASNSYNB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUPEROX-DISMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUPEROX-DISMUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5407| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5407| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-SYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|O-SUCCINYLBENZOATE-COA-SYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMINEOXID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINEOXID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-383| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-383| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17790| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17790| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-161| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-161| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANSENOYLCOARED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANSENOYLCOARED-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15131| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15131| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-236| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-236| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NARX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NARX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RHAMNULOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RHAMNULOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5268| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5268| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPCARBTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPCARBTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THREONINE-ALDOLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREONINE-ALDOLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-278| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-278| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARGSUCCINLYA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGSUCCINLYA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DSERDEAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSERDEAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-297| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-297| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5039| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5039| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4341| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4341| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-330| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-330| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15346| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15346| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5510| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5510| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-351| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-351| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15881| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15881| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OHMETHYLBILANESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHMETHYLBILANESYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-368| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-368| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TREHALOSEPHOSPHA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALOSEPHOSPHA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17900| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17900| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-62A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PABASYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PABASYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ATPPHOSPHORIBOSYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPPHOSPHORIBOSYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.6.1.82-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.6.1.82-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5057| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5057| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10015| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10015| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TSA-REDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TSA-REDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15952| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15952| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-212| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-212| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PDXJ-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PDXJ-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ENTMULTI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTMULTI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERVAL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERVAL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALA-GLU-LIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMURALA-GLU-LIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-265| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-265| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CARDIOLIPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARDIOLIPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6388| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6388| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7050| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7050| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5103| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5103| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5116| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5116| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-282| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-282| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16649| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16649| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18032| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18032| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-454| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-454| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16424| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16424| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHENDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-475| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-475| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UREIDOGLYCOLATE-LYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UREIDOGLYCOLATE-LYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11326| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11326| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7206| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7206| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGPPHOSPHA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGPPHOSPHA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|COBINAMIDEKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBINAMIDEKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-12-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-12-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5182| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5182| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FUCISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUCISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-496| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-496| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UGD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UGD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16909| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16909| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ISOCITDEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCITDEH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLUCMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOGLUCMUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6484| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6484| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-32-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-32-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CITRATE-PRO-3S-LYASE-THIOLESTERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CITRATE-PRO-3S-LYASE-THIOLESTERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|YIAE1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|YIAE1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-513| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-513| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|D--TARTRATE-DEHYDRATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|D--TARTRATE-DEHYDRATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.283-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.283-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2481| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2481| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5141| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5141| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5214| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5214| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-532| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-532| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17392| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17392| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18708| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18708| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-535| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-535| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16701| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16701| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRODISULFREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-557| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-557| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXPHOSGALACT-ALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXPHOSGALACT-ALDOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11593| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11593| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-574| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-574| ))\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-122| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYTIDEAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDEAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5383| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5383| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-142| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-142| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17782| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17782| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-OHPHENOL-METHY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OCTAPRENYL-6-OHPHENOL-METHY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-167| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5208| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5208| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R165-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R165-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17663| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17663| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIOHBUTANONEPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIOHBUTANONEPSYN-RXN| ))\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17798| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11835| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11835| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRAISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRAISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOPHOSPHAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-337| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-337| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DURIDKI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DURIDKI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-6-P-DEAMIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSAMINE-6-P-DEAMIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6370| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6370| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DCTP-PYROPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCTP-PYROPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6277| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6277| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-354| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-354| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17931| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17931| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6565| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6565| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-372| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-372| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5234| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5234| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10819| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10819| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-69| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-69| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FCLEPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FCLEPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.1.121-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.1.121-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-0244| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-0244| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17633| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17633| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10940| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10940| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-222| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-222| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FHLMULTI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FHLMULTI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19775| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19775| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-268| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-268| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PSEUDOURIDINE-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PSEUDOURIDINE-KINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-286| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-286| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18392| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18392| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12071| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12071| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-460| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-460| ))\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-15-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-15-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17778| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17778| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19004| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19004| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-499| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-499| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11637| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11637| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-DEHYDROQUINATE-DEHYDRATASE-RXN| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-2881| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2881| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-35-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-35-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.3.1.118-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.3.1.118-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-517| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-517| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19407| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19407| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12458| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12458| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2542| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2542| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5413| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5413| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11843| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11843| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-538| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-538| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTAMIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCOLATEDEHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLATEDEHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-560| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-560| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17794| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17794| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6717| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6717| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-577| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-577| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.8.25-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.8.25-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6978| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6978| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-598| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-598| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19922| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19922| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-622| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-622| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12197| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12197| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.21.3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108F| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108F| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DTDPGLUCOSEPP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPGLUCOSEPP-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCEROL-1-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCEROL-1-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6950| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6950| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-6622| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6622| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5130| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5130| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6259| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6259| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.11.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.11.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-146| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-146| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-5647| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5647| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12864| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12864| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5201| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5201| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17918| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17918| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12611| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12611| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-169| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-169| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOXYLATE-REDUCTASE-NADP+-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXYLATE-REDUCTASE-NADP+-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GSAAMINOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSAAMINOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10040| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10040| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6987| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6987| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-284| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-284| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.27.5-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.27.5-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-300| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-300| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|EXOPOLYPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|EXOPOLYPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7800| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7800| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-340| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-340| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12896| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12896| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.2.2.10-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.2.2.10-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6375| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6375| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6444| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6444| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GUANINE-DEAMINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANINE-DEAMINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-357| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-357| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7020| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7020| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8340| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6491| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6491| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6451| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6451| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.13.21-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.21-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-378| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-378| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8632| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8632| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13418| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13418| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19778| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19778| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18241| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18241| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13859| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13859| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-76| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-76| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HISTCYCLOHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTCYCLOHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|H2NTPEPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|H2NTPEPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-200| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-200| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11410| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11410| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7079| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7079| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-227| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-227| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.24.70-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.24.70-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7046| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7046| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13179| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13179| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GABATRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GABATRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9559| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9559| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-272| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-272| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14115| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14115| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.107-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.107-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7077| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7077| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6494| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6494| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|IMIDPHOSDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IMIDPHOSDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-418| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-418| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7141| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7141| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8974| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8974| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7123| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7123| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.13.11.16-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.13.11.16-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5-OXOPROLINASE-ATP-HYDROLYSING-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-OXOPROLINASE-ATP-HYDROLYSING-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.6.3.53-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.53-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1402| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1402| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14064| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14064| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-463| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-463| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18738| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18738| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14260| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14260| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7189| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7189| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KDO-8PSYNTH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDO-8PSYNTH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOMOSERDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOSERDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1682| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1682| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11601| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11601| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7235| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7235| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-486| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-486| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETATEKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETATEKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7102| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7102| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7215| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7215| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDPMANMANHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPMANMANHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2023| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2023| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1924| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1924| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14396| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14396| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.1.2.28-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.1.2.28-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-19-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-19-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6529| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6529| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LCARNCOALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LCARNCOALIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-502| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-502| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7304| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7304| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7246| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7246| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.1.1.34-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.34-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACONITATEDEHYDR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACONITATEDEHYDR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-4-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-4-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2604| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2604| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14160| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14160| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-520| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-520| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19341| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19341| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14509| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14509| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-541| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-541| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-ACCEPTOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALATE-DEHYDROGENASE-ACCEPTOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|IPPISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IPPISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-563| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-563| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11839| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11839| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|S-ADENMETSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|S-ADENMETSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15294| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15294| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENYLATECYC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENYLATECYC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7170| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7170| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-580| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-580| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2943| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2943| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-603| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-603| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14693| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14693| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|6-PHOSPHO-BETA-GLUCOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|6-PHOSPHO-BETA-GLUCOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-100| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-100| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6676| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6676| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHENYLTHFCYCLOHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHENYLTHFCYCLOHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108I| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108I| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCARGDIHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCARGDIHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1861| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1861| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5111| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5111| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.7.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-127| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-127| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3261| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3261| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14290| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14290| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-155| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19854| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19854| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14904| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14904| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5205| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5205| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NACGLCTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NACGLCTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KETOGLUTREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOGLUTREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-20| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-20| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12104| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12104| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TARTRATE-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TARTRATE-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-261| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-261| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMINOCYL-TRNA-HYDROLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINOCYL-TRNA-HYDROLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7270| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7270| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-29| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTSEMIALDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTSEMIALDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3901| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3901| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-312| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-312| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15147| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15147| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETYL-COA-ACETYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYL-COA-ACETYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-344| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-344| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6941| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6941| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NICOTINATEPRIBOSYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICOTINATEPRIBOSYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-361| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-361| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THTOREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THTOREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2281| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2281| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-41| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-41| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARYLSULFAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARYLSULFAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-81| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-81| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4401| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4401| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14480| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14480| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-5076| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5076| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-3521| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3521| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15358| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15358| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-203| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-203| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ORNDECARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ORNDECARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LUMAZINESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LUMAZINESYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-235| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-235| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12540| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12540| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRNA-CYTIDYLYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-CYTIDYLYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-275| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-275| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BARA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BARA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-963| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-963| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-446| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-446| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOHMETRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOHMETRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16003| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16003| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-466| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-466| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PEPDEPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEPDEPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADDALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADDALT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7199| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7199| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6982| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6982| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPACYLGLCNACDEACETYL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPACYLGLCNACDEACETYL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1701| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1701| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CDPDIGLYPYPHOSPHA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CDPDIGLYPYPHOSPHA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-271| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-271| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-491| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-491| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.26.12-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.12-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5121| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5121| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7221| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7221| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16660| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16660| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14522| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14522| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1982| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1982| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7607| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7607| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHENYLPYRUVATE-TAUTOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHENYLPYRUVATE-TAUTOMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-23-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-23-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|URKI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URKI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-505| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-505| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12872| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12872| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CPXA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CPXA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-56-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-56-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5185| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5185| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-5-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SHIKIMATE-5-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-524| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-524| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GST-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GST-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16938| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16938| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-546| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-546| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PNKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PNKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AIRS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AIRS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-566| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-566| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7010| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7010| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DAHPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DAHPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-586| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-586| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5220| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5220| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-305| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-305| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15740| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15740| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.11.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17473| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17473| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-607| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-607| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROPIONYL-COA-CARBOXY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROPIONYL-COA-CARBOXY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14810| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14810| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-105| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-105| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8460| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8460| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEOXYGUANPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYGUANPHOSPHOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-114| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-114| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5295| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5295| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-131| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-131| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13747| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13747| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17725| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17725| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-157| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-157| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRIMSYN1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRIMSYN1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCSEMIALDDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCSEMIALDDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-218| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-218| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HEMEOSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HEMEOSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMEPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIAMINOPIMEPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5256| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5256| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5391| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5391| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALPHA-AMYL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALPHA-AMYL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-27| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-27| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7068| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7068| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17785| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17785| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-292| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-292| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R4-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R4-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3601| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6367| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6367| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIOESTER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIOESTER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-206| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-206| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HYDROXYLAMINE-REDUCTASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDROXYLAMINE-REDUCTASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17944| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17944| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-240| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-240| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11135| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11135| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARCB717-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARCB717-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8638| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8638| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7115| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7115| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FORMYLTHFDEFORMYL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FORMYLTHFDEFORMYL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-278| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-278| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6479| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6479| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4222| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4222| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-449| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-449| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.3.1.17-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.3.1.17-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.215-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.215-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-469| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-469| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18550| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18550| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15299| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15299| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7202| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7202| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1321| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14196| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14196| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6518| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6518| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-26-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-26-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-DEHYDROPANTOATE-REDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-DEHYDROPANTOATE-REDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANSALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANSALDOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5038| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5038| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-550| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-550| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|7KAPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|7KAPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.4.1.78-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.4.1.78-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-570| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-570| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19573| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19573| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15878| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15878| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-589| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-589| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1922| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1922| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11865| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11865| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-610| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-610| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-PEROXIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTATHIONE-PEROXIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSLIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|P-PANTOCYSLIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-106B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14379| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14379| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6722| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6722| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-118| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-118| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.9.1.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.9.1.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPTOPHAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-14| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-14| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|L-LACTDEHYDROGFMN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-LACTDEHYDROGFMN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19954| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19954| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-16| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-16| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12275| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12275| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERLEU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BRANCHED-CHAINAMINOTRANSFERLEU-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-23| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-23| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7283| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7283| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5266| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5266| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6973| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6973| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5101| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5101| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-277| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-277| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETYLORNTRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLORNTRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.13.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.13.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5330| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5330| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-6081| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6081| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16420| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16420| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-296| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-296| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12753| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12753| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-33| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-33| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GMP-REDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GMP-REDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSII-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCEROLTRANSII-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-350| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-350| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14500| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14500| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6992| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6992| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19020| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19020| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.3.74-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.3.74-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPSUGARHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPSUGARHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-367| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-367| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LYSOPHOSPHOLIPASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSOPHOSPHOLIPASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7948| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7948| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-61| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-61| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13142| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13142| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHORPYRLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORPYRLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-94A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN1-42| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN1-42| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GUANPRIBOSYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GUANPRIBOSYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-211| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-211| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7023| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7023| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5131| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5131| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-264| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-264| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.15.5-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.15.5-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13519| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13519| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8654| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8654| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16691| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16691| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-281| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-281| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-280| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-280| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14014| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14014| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-453| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-453| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHAGLYPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHAGLYPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HISTOLDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTOLDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-474| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-474| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|XANPRIBOSYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XANPRIBOSYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14534| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14534| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7083| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7083| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7205| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7205| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYTDEAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTDEAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.6.1.41-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.1.41-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1804| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1804| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5200| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5200| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNPDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNPDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9597| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9597| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-11-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-11-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17010| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17010| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14126| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14126| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PPPGPPHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPPGPPHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SORBITOL-6-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SORBITOL-6-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|INOPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOPHOSPHOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-512| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-512| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DCTP-DEAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCTP-DEAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7160| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7160| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5229| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5229| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALANINE-AMINOTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALANINE-AMINOTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5.3.3.14-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.3.3.14-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-9-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-9-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17632| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17632| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1483| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1483| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-530| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-530| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PSERTRANSAMPYR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PSERTRANSAMPYR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3182| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3182| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14282| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14282| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN66-448| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN66-448| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DGTPTRIPHYDRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DGTPTRIPHYDRO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KDPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDPD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-534| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-534| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5359| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5359| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14815| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14815| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7248| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7248| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-556| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-556| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17777| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17777| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETOINDEHYDROG-A-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOINDEHYDROG-A-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3501| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3501| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|QOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MMUM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MMUM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2061| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2061| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-573| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-573| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDROOROT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROOROT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14461| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14461| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-592| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-592| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5410| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5410| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SULFOCYS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFOCYS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LEUCYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LEUCYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-614| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-614| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17793| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17793| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-743| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-743| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVIN-SYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVIN-SYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMACETOXID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMACETOXID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACYL-COA-HYDROLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYL-COA-HYDROLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121C| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-121C| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DTDPGLUCDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTDPGLUCDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-262| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-262| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-141B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6256| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6256| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14512| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14512| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-165| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-165| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17916| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17916| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17652| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17652| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10018| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10018| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15129| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15129| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SAMDECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SAMDECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-238| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-238| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ETHAMLY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ETHAMLY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADOMET-DMK-METHYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADOMET-DMK-METHYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-280| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-280| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6427| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6427| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18232| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18232| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THREONINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREONINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHIONYL-TRNA-FORMYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHIONYL-TRNA-FORMYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6369| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6369| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11409| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11409| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCGLUALDDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCGLUALDDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-353| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-353| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FUMHYDR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FUMHYDR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARGININE-N-SUCCINYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGININE-N-SUCCINYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALDOSE1EPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALDOSE1EPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-371| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-371| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6493| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6493| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-68| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-68| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.11.1.15-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.11.1.15-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4301| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4301| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14997| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14997| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-99| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-99| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18737| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18737| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-NH3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAD-SYNTH-NH3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-214| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-214| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11600| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11600| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15345| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15345| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TETRAACYLDISACC4KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TETRAACYLDISACC4KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-267| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-267| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GDPMANDEHYDRA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GDPMANDEHYDRA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMP-NUCLEOSID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMP-NUCLEOSID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-284| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-284| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6528| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6528| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OHBUTYRYL-COA-EPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHBUTYRYL-COA-EPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3942| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3942| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-459| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-459| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-OXOPENT-4-ENOATE-HYDRATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-OXOPENT-4-ENOATE-HYDRATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15292| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15292| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7185| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7185| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19338| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19338| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TREHALOSE6PSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALOSE6PSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NQOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NQOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-16| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-16| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11838| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11838| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THYMIDYLATE-5-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THYMIDYLATE-5-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-478| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-478| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCOSE-6-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ATPASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPARAGHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARAGHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7208| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7208| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6576| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6576| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4641| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4641| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-14-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-14-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.13.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.13.2-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5052| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5052| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15581| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15581| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-498| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-498| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19793| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19793| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OXALOACETATE-TAUTOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXALOACETATE-TAUTOMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7242| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7242| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12093| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12093| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15943| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15943| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRNA-PSEUDOURIDINE-SYNTHASE-I-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRNA-PSEUDOURIDINE-SYNTHASE-I-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2162| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2162| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTRNAREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTRNAREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BETA-LACTAMASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BETA-LACTAMASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-34-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-34-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6938| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6938| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PANTOTHENATE-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTOTHENATE-KIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5063| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5063| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-515| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-515| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-ISOPROPYLMALDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16225| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16225| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2522| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2522| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-3482| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3482| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDP-NACMUR-ALA-LIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDP-NACMUR-ALA-LIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PEROXID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PEROXID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-537| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-537| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12539| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12539| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-559| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-559| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOCARBOLIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOCARBOLIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CARBOXYLESTERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARBOXYLESTERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CELLULOSE-SYNTHASE-UDP-FORMING-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CELLULOSE-SYNTHASE-UDP-FORMING-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-576| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-576| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6981| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6981| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5124| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5124| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-596| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-596| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.26.11-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.11-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5114| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5114| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16685| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16685| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7605| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7605| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOR-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-617| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-617| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12871| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12871| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16475| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16475| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UROPORIIIMETHYLTRANSA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UROPORIIIMETHYLTRANSA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108E| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108E| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GSPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GSPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CTPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CTPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-123| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-123| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7008| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7008| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|URACIL-PRIBOSYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|URACIL-PRIBOSYLTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5189| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5189| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-145| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-145| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.11.18-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.18-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16996| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16996| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-168| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-168| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8348| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8348| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|COBALAMIN5PSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|COBALAMIN5PSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-242| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13548| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13548| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DARAB5PISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARAB5PISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-283| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-283| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HCAMULTI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HCAMULTI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5181| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5181| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5224| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5224| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-30| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-30| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7067| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7067| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17493| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17493| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIMESULFREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIMESULFREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.87-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.87-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16804| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16804| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PROTOPORGENOXI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PROTOPORGENOXI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-339| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-339| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8999| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8999| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6373| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6373| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14074| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14074| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOENOLPYRUVATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOENOLPYRUVATE-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5304| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5304| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-356| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-356| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HYDGLUTSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HYDGLUTSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17752| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17752| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-377| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-377| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7114| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7114| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|XYLULOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLULOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYROXALTRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYROXALTRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-72| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-72| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4.3.1.15-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4.3.1.15-RXN| ))\n", - 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"(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-181| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14188| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14188| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17788| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17788| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-226| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-226| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ISOCIT-CLEAV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ISOCIT-CLEAV-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5213| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5213| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RFFTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RFFTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13163| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13163| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7188| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7188| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-RNA-POLYMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DNA-DIRECTED-RNA-POLYMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-270| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-270| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|7-ALPHA-HYDROXYSTEROID-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|7-ALPHA-HYDROXYSTEROID-DEH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17391| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17391| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5507| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5507| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-417| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-417| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1882| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1882| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17886| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17886| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-10| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-10| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14363| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14363| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRIBFAICARPISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRIBFAICARPISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RNA-3-PHOSPHATE-CYCLASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RNA-3-PHOSPHATE-CYCLASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.6.3.39-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.6.3.39-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|L-IDONATE-2-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|L-IDONATE-2-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ENTDB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ENTDB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-462| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-462| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7280| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7280| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXGALACTKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DEHYDDEOXGALACTKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-481| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-481| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETYLORNDEACET-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETYLORNDEACET-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17956| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17956| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7211| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7211| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5289| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5289| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17962| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17962| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1923| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1923| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14497| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14497| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11313| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11313| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-18-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-18-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LYSINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYSINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17636| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17636| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FRUCTOKINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FRUCTOKINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-501| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-501| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-986| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-986| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6482| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6482| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7245| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7245| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENOSINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENOSINE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRAMKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRAMKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.1.1.271-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.1.1.271-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-37-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-37-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-279| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-279| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18703| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18703| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-519| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-519| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14525| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14525| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DHHB-METHYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHHB-METHYLTRANSFER-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11591| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11591| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-540| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-540| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MANNOSE-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MANNOSE-ISOMERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GART-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GART-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-562| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-562| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SORB6PDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SORB6PDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5375| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5375| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6523| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6523| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-579| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-579| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALANINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALANINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-SYNTHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2-METHYLCITRATE-SYNTHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-601| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-601| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-313| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-313| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17781| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17781| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19253| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19253| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-10| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-10| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14813| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14813| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11833| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11833| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-628| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-628| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MHPHYDROXY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MHPHYDROXY-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|R15-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|R15-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUCONOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUCONOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108H| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-108H| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SULFITE-REDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SULFITE-REDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6563| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6563| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126B| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-126B| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALTRODEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALTRODEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIMETHUROPORDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIMETHUROPORDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.6.1.57-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.6.1.57-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CARBPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CARBPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3741| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19630| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19630| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153A| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-153A| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15127| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15127| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5422| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5422| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12002| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12002| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5203| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5203| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NAPHTHOATE-SYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NAPHTHOATE-SYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTCYSLIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTCYSLIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-2| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-2| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THREODEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREODEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17797| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17797| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6727| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6727| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-250| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-250| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARGININE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGININE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2TRANSKETO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2TRANSKETO-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-286| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-286| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4281| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4281| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-2043| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-2043| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-310| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-310| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15341| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15341| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12444| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12444| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGFAD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DLACTDEHYDROGFAD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OHACYL-COA-DEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OHACYL-COA-DEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DUDPKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DUDPKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCOLALD-DEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCOLALD-DEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-342| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-342| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TREHALA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TREHALA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6976| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6976| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-360| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-360| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ATP-PYROPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATP-PYROPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6274| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6274| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.21.1-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.21.1-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6511| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6511| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5051| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5051| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-6321| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-6321| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11496| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11496| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15925| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15925| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17930| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17930| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12861| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12861| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-40| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-40| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PANTOATE-BETA-ALANINE-LIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PANTOATE-BETA-ALANINE-LIG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GPH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GPH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5146| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5146| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FGAMSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FGAMSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.21.102-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.21.102-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7191| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7191| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16788| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16788| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8770| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8770| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-17| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-17| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSPHOAMIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSPHOAMIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6460| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6460| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14026| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14026| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-490| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-490| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|XYLONATE-DEHYDRATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|XYLONATE-DEHYDRATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HOMOCYSMETB12-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HOMOCYSMETB12-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1981| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1981| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYTIDINEKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTIDINEKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18388| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18388| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7100| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7100| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-20-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-20-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5210| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5210| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-504| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-504| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17330| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17330| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11573| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11573| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9952| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9952| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-5-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-5-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PREPHENATEDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14142| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14142| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-523| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-523| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DCYSDESULF-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DCYSDESULF-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|INOSINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|INOSINE-NUCLEOSIDASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GALACTOKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTOKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-545| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-545| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5285| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5285| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7167| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7167| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-565| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-565| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17635| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17635| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6509| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6509| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5.99.1.2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5.99.1.2-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-585| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-585| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PUTTRANSAM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PUTTRANSAM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1661| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1661| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-606| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-606| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DHDOGALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DHDOGALDOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.5.1.34-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.5.1.34-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14285| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14285| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-104| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-104| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5364| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5364| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KETOACYLCOATHIOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KETOACYLCOATHIOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-113| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-113| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17780| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17780| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18999| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18999| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7251| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7251| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ATPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ATPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|QUINOPRIBOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|QUINOPRIBOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTREDUCTOISOM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETOOHBUTREDUCTOISOM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-130| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-130| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DIHYDROXYMETVALDEHYDRAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DIHYDROXYMETVALDEHYDRAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11635| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11635| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2161| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2161| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-156| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-156| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5418| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5418| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14478| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14478| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-21| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-21| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17796| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17796| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLCNACPTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLCNACPTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LTAA-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LTAA-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DALADEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DALADEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNREDUC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RIBOFLAVINSYNREDUC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-961| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-961| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-267| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-267| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DTMPKI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DTMPKI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6541| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6541| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACYLPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACYLPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-291| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-291| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6272| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6272| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2661| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2661| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-320| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-320| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17920| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17920| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.1.1.79-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.79-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14515| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14515| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-347| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-347| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-10720| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-10720| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MALTODEXGLUCOSID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MALTODEXGLUCOSID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-363| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-363| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|F16BDEPHOS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|F16BDEPHOS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19381| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19381| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SERINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SERINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FORMATEDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FORMATEDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|FCLREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|FCLREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AICARSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AICARSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-44| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-44| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6459| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6459| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11842| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11842| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-303| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-303| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-86| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN-86| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18376| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18376| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14808| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14808| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-205| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-205| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11484| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11484| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLUTAMIDOTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLUTAMIDOTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-EPIM-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|METHYLMALONYL-COA-EPIM-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-239| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-239| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GALACTOACETYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GALACTOACETYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SUCCINYLDIAMINOPIMTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SUCCINYLDIAMINOPIMTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13403| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13403| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6506| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6506| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6710| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6710| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALLANTOINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALLANTOINASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-448| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-448| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|1.5.1.20-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|1.5.1.20-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3542| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3542| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-14| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-14| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-18819| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-18819| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.7.8-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.8-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15121| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15121| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-468| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-468| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11633| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11633| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NADPYROPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NADPYROPHOSPHAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7201| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7201| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GKI-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GKI-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19921| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19921| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN3-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THIAZOLSYN3-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1721| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1721| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6532| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6532| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ANTHRANSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ANTHRANSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-493| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-493| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.1.1.77-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.1.1.77-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12195| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12195| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4121| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-25-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-25-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19362| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19362| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15297| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15297| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-508| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-508| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-11841| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-11841| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYCDEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYCDEH-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NUCLEOTIDE-PYROPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NUCLEOTIDE-PYROPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ABC-64-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ABC-64-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLURS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLURS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-277| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-277| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-526| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRANS-RXN0-526| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6708| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6708| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6948| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6948| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ASPARTATE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ASPARTATE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|2.7.7.60-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|2.7.7.60-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-19920| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-19920| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15744| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15744| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12149| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12149| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|OXAMATE-CARBAMOYLTRANSFERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|OXAMATE-CARBAMOYLTRANSFERASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYC3PDEHYDROGBIOSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYC3PDEHYDROGBIOSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-4821| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-4821| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TRYPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TRYPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6945| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6945| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|BIS5-ADENOSYL-TRIPHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|BIS5-ADENOSYL-TRIPHOSPHATASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12587| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12587| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5074| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5074| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-3641| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-3641| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16286| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16286| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12583| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12583| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOXIII-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXIII-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PGLYCDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PGLYCDEHYDROG-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GLYOXII-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GLYOXII-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6984| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6984| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6985| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6985| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CHORISMATE-SYNTHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CHORISMATE-SYNTHASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.26.4-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.4-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5127| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5127| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7632| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7632| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.1.26.5-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.1.26.5-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-16689| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-16689| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12886| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12886| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PHOSMANMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PHOSMANMUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-II-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTP-CYCLOHYDRO-II-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-7682| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-7682| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|VALINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|VALINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7013| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7013| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYSTEINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYSTEINE--TRNA-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.11.9-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.11.9-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-12895| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-12895| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5195| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5195| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-8487| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-8487| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17008| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17008| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13853| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13853| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|GTPPYPHOSKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|GTPPYPHOSKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PPENTOMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PPENTOMUT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|HISTALDEHYD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|HISTALDEHYD-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DARABKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DARABKIN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7075| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7075| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7014| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7014| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5227| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5227| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17928| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17928| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.23.43-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.23.43-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17630| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17630| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17910| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17910| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-9310| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-9310| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.13.18-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.13.18-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PRTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PRTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14112| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17775| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17775| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5-FORMYL-THF-CYCLO-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-FORMYL-THF-CYCLO-LIGASE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-13854| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-13854| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|PYRUVATEDECARB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|PYRUVATEDECARB-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1382| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1382| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2001| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2001| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|3.4.24.55-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|3.4.24.55-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-5515| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-5515| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14393| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14393| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-17905| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-17905| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LACTALDDEHYDROG-RXN| )\n", - 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"cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14113| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14113| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-6389| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-6389| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2584| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2584| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14503| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14503| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|IGPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|IGPSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|LYXK-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|LYXK-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXNMETA-12671| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXNMETA-12671| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7139| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7139| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ADENPRIBOSYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ADENPRIBOSYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2941| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2941| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|5-NUCLEOTID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|5-NUCLEOTID-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14569| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14569| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MERCAPYSTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MERCAPYSTRANS-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1401| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1401| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|SPERMIDINESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|SPERMIDINESYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7049| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7049| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14255| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14255| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-1130| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-1130| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3221| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3221| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|UBIQUINOL-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|UBIQUINOL-OX-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14882| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14882| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|KDO-8PPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|KDO-8PPHOSPHAT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DMK-FE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSBDC-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|TAGAALDOL-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7230| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|MEN-FE-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|AMINEPHEN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7048| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-384| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ACETATE--COA-LIGASE-RXN| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7096| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-15139| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-5068| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-2022| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-7310| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|THREOSPON-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|CYTC-RED-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|ARGSUCCINSYN-RXN| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN-14394| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-3141| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|RXN0-4342| ))\n", - "cofactors-and-pgroups-of-enzrxn\n", - "(cofactors-and-pgroups-of-enzrxn '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (cofactors-and-pgroups-of-enzrxn '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = 'all'):\n", - " lst.append(ecoli.cofactors_and_pgroups_of_enzrxn(enzrxn = enzrxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-15348| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-15348| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|LACTALDREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|LACTALDREDUCT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PFLDEACTIV-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PFLDEACTIV-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|OHMETPYRKIN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|OHMETPYRKIN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7094| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7094| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|TRIOSEPISOMERIZATION-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TRIOSEPISOMERIZATION-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7298| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7298| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-1137| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-1137| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|BADH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|BADH-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|DMKCYT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DMKCYT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5061| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5061| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|ACONITATE-DELTA-ISOMERASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACONITATE-DELTA-ISOMERASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|FES-OX-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|FES-OX-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16000| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16000| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-6505| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6505| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PEPCARBOX-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PEPCARBOX-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-2601| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2601| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|MENCYT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MENCYT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|UDP-NACMURALGLDAPAALIG-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|UDP-NACMURALGLDAPAALIG-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7003| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7003| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|CARNDETRU-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|CARNDETRU-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-14505| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14505| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|ADPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ADPREDUCT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5118| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5118| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|CHEBTAPD-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|CHEBTAPD-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16650| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16650| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|MALATE-DEH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MALATE-DEH-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|DEPHOSICITDEHASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DEPHOSICITDEHASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PHENPRODIOLDEHYDROG-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PHENPRODIOLDEHYDROG-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|GDPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|GDPREDUCT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|URIDINE-NUCLEOSIDASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|URIDINE-NUCLEOSIDASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXNMETA-12672| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXNMETA-12672| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|MYRISTOYLACYLTRAN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MYRISTOYLACYLTRAN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|COBINPGUANYLYLTRANS-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|COBINPGUANYLYLTRANS-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PROTEIN-KINASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PROTEIN-KINASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5183| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5183| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|ADENYL-KIN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ADENYL-KIN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-10658| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-10658| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16910| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16910| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-12473| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-12473| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-2942| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2942| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16381| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16381| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|YIAE2-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|YIAE2-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-17355| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-17355| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|D-PPENTOMUT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|D-PPENTOMUT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-14570| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14570| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-19340| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-19340| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5216| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5216| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-5741| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-5741| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-17393| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-17393| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|METBALT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|METBALT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-9533| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-9533| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PROLINE--TRNA-LIGASE-RXN| t )\n", - 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"(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-17936| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-20000| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-20000| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|R167-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|R167-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16009| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16009| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-9532| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-9532| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-287| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-287| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|PEPSYNTH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|PEPSYNTH-RXN| t ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-11109| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-11109| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-9659| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-9659| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-4462| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-4462| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|UDPGLCNACEPIM-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|UDPGLCNACEPIM-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-1141| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-1141| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5347| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5347| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|CDPDIGLYSYN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|CDPDIGLYSYN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|FOLYLPOLYGLUTAMATESYNTH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|FOLYLPOLYGLUTAMATESYNTH-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5055| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5055| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5487| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5487| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-5122| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-5122| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-6546| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6546| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-6989| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6989| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-16664| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-16664| t ))\n", - 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"name": "stdout", - "output_type": "stream", - "text": [ - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6506| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-6710| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-6710| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|ALLANTOINASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ALLANTOINASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|TRANS-RXN0-448| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TRANS-RXN0-448| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|1.5.1.20-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|1.5.1.20-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-3542| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-3542| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-14| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-14| t ))\n", - 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"(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|UBIQUINOL-OX-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-14882| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14882| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|KDO-8PPHOSPHAT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|KDO-8PPHOSPHAT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|DMK-FE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DMK-FE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|N-ACETYLGLUTPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|N-ACETYLGLUTPREDUCT-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|DSBDC-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DSBDC-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|TAGAALDOL-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|TAGAALDOL-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7230| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7230| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|MEN-FE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|MEN-FE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|AMINEPHEN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|AMINEPHEN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7048| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7048| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-384| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-384| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|ACETATE--COA-LIGASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ACETATE--COA-LIGASE-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7096| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7096| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-15139| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-15139| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-5068| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-5068| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|NICONUCADENYLYLTRAN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|NICONUCADENYLYLTRAN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-2022| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-2022| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-7310| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-7310| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|THREOSPON-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|THREOSPON-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|CYTC-RED-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|CYTC-RED-RXN| t ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzrxn-activators\n", - "(enzrxn-activators '|ARGSUCCINSYN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|ARGSUCCINSYN-RXN| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN-14394| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN-14394| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-3141| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-3141| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|RXN0-4342| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|RXN0-4342| t ))\n", - "enzrxn-activators\n", - "(enzrxn-activators '|DSBD-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-activators '|DSBD-RXN| t ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "er\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "phys-relevant-only?\n", - "Optional If true, then only return activators that are associated with \n", - "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", - "non-nil. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.enzrxn_activators(enzrxn = enzrxn, phys_relevant_only=True))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-15348| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-15348| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|LACTALDREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|LACTALDREDUCT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PFLDEACTIV-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PFLDEACTIV-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|OHMETPYRKIN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|OHMETPYRKIN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7094| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7094| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|TRIOSEPISOMERIZATION-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|TRIOSEPISOMERIZATION-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7298| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7298| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-1137| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-1137| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|BADH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|BADH-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DMKCYT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DMKCYT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5061| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5061| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ACONITATE-DELTA-ISOMERASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ACONITATE-DELTA-ISOMERASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|FES-OX-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|FES-OX-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-16000| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-16000| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-6505| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-6505| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PEPCARBOX-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PEPCARBOX-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-2601| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2601| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|MENCYT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MENCYT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|UDP-NACMURALGLDAPAALIG-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|UDP-NACMURALGLDAPAALIG-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7003| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7003| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|CARNDETRU-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|CARNDETRU-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-14505| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14505| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ADPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ADPREDUCT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5118| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5118| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|CHEBTAPD-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|CHEBTAPD-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-16650| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-16650| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|MALATE-DEH-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MALATE-DEH-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DEPHOSICITDEHASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DEPHOSICITDEHASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PHENPRODIOLDEHYDROG-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PHENPRODIOLDEHYDROG-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|GDPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|GDPREDUCT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|URIDINE-NUCLEOSIDASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|URIDINE-NUCLEOSIDASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXNMETA-12672| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXNMETA-12672| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|MYRISTOYLACYLTRAN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MYRISTOYLACYLTRAN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|COBINPGUANYLYLTRANS-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|COBINPGUANYLYLTRANS-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PROTEIN-KINASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PROTEIN-KINASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5183| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5183| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ADENYL-KIN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ADENYL-KIN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-10658| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-10658| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-16910| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-16910| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-12473| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-12473| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-2942| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2942| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-16381| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-16381| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|YIAE2-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|YIAE2-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-17355| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17355| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|D-PPENTOMUT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|D-PPENTOMUT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-14570| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14570| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-19340| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-19340| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5216| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5216| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-5741| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-5741| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-17393| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17393| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|METBALT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|METBALT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-9533| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-9533| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|PROLINE--TRNA-LIGASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|PROLINE--TRNA-LIGASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-9660| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-9660| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DEOXYADENPHOSPHOR-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DEOXYADENPHOSPHOR-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|SPONTPRO-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|SPONTPRO-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-1144| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-1144| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5292| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5292| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-5098| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-5098| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-17701| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-17701| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ALCOHOL-DEHYDROG-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ALCOHOL-DEHYDROG-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-6435| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-6435| t ))\n", - 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"enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DMK-FE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DMK-FE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|N-ACETYLGLUTPREDUCT-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|N-ACETYLGLUTPREDUCT-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DSBDC-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DSBDC-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|TAGAALDOL-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|TAGAALDOL-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7230| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7230| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|MEN-FE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|MEN-FE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|AMINEPHEN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|AMINEPHEN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7048| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7048| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-384| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-384| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ACETATE--COA-LIGASE-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ACETATE--COA-LIGASE-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7096| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7096| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-15139| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-15139| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-5068| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-5068| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|NICONUCADENYLYLTRAN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|NICONUCADENYLYLTRAN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-2022| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-2022| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-7310| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-7310| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|THREOSPON-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|THREOSPON-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|CYTC-RED-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|CYTC-RED-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|ARGSUCCINSYN-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|ARGSUCCINSYN-RXN| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN-14394| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN-14394| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-3141| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-3141| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|RXN0-4342| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|RXN0-4342| t ))\n", - "enzrxn-inhibitors\n", - "(enzrxn-inhibitors '|DSBD-RXN| t )\n", - "(with-organism (:org-id '|ECOLI|) (enzrxn-inhibitors '|DSBD-RXN| t ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.enzrxn_inhibitors(enzrxn = enzrxn, phys_relevant_only = True))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-15348| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-15348| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|LACTALDREDUCT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|LACTALDREDUCT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|PFLDEACTIV-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PFLDEACTIV-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|OHMETPYRKIN-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|OHMETPYRKIN-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-7094| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7094| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|TRIOSEPISOMERIZATION-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-7298| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7298| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-1137| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-1137| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|BADH-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|BADH-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|DMKCYT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|DMKCYT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-5061| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-5061| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ACONITATE-DELTA-ISOMERASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|FES-OX-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|FES-OX-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-16000| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-16000| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-6505| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-6505| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|PEPCARBOX-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PEPCARBOX-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-2601| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-2601| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|MENCYT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|MENCYT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|UDP-NACMURALGLDAPAALIG-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-7003| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7003| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|CARNDETRU-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|CARNDETRU-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-14505| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-14505| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|ADPREDUCT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ADPREDUCT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-5118| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-5118| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|CHEBTAPD-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|CHEBTAPD-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-16650| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-16650| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|MALATE-DEH-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|MALATE-DEH-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|DEPHOSICITDEHASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|DEPHOSICITDEHASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PHENPRODIOLDEHYDROG-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|GDPREDUCT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|GDPREDUCT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|URIDINE-NUCLEOSIDASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXNMETA-12672| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXNMETA-12672| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|MYRISTOYLACYLTRAN-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|COBINPGUANYLYLTRANS-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|PROTEIN-KINASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PROTEIN-KINASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-5183| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-5183| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|ADENYL-KIN-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ADENYL-KIN-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-10658| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-10658| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-16910| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-16910| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-12473| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-12473| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-2942| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-2942| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-16381| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-16381| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|YIAE2-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|YIAE2-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-17355| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-17355| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|D-PPENTOMUT-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|D-PPENTOMUT-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-14570| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-14570| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-19340| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-19340| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-5216| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-5216| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-5741| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-5741| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-17393| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-17393| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|METBALT-RXN| :include-super-pwys? nil)\n", - 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"pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-384| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-384| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|ACETATE--COA-LIGASE-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ACETATE--COA-LIGASE-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-7096| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7096| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-15139| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-15139| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-5068| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-5068| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|NICONUCADENYLYLTRAN-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-2022| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-2022| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-7310| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-7310| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|THREOSPON-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|THREOSPON-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|CYTC-RED-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|CYTC-RED-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|ARGSUCCINSYN-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|ARGSUCCINSYN-RXN| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN-14394| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN-14394| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-3141| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-3141| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|RXN0-4342| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|RXN0-4342| :include-super-pwys? nil))\n", - "pathways-of-enzrxn\n", - "(pathways-of-enzrxn '|DSBD-RXN| :include-super-pwys? nil)\n", - "(with-organism (:org-id '|ECOLI|) (pathways-of-enzrxn '|DSBD-RXN| :include-super-pwys? nil))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "enzrxn\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "include-super-pwys?\n", - "Keyword, Optional If non-nil, then not only will the direct pathways in which \n", - "enzrxn is associated in be returned, but also any enclosing super-pathways. If \n", - "enzrxn is associated with a reaction that is directly associated with a \n", - "super-pathway, then the function might return super-pathways even if this option \n", - "is nil.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.pathways_of_enzrxn(enzrxn = enzrxn, include_super_pwys = False))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "all-rxns\n", - "(all-rxns :all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns :all ))\n", - "all-rxns\n", - "(all-rxns :metab-smm )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns :metab-smm ))\n", - "pathway-allows-enzrxn\\?\n", - "(pathway-allows-enzrxn\\? '|PWY0-1347| '|RXN-15348| '|RXN-15348| '|ECOLI| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-allows-enzrxn\\? '|PWY0-1347| '|RXN-15348| '|RXN-15348| '|ECOLI| ))\n" - ] - }, - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1640\u001b[0m \t\t\"\"\"\n\u001b[1;32m 1641\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1642\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn\\\\?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1643\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 375\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 376\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 377\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 367\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 368\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 369\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 370\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 357\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m') '\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mquery\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 358\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 359\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 360\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 361\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." - ] - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "enzrxn\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "single-species\n", - "Optional An instance of the class |Organisms| If set, then enzrxn has the \n", - "further stricture that it must be an enzymatic reaction present in the organism \n", - "specified by the value passed to single‑species.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " for rxn1 in ecoli.all_rxns(type_of_reactions = 'all'):\n", - " for rxn2 in ecoli.all_rxns(type_of_reactions = 'metab-smm'):\n", - " lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n", - " pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/ptools API - Operations on Pathways.ipynb b/examples/ptools API - Operations on Pathways.ipynb deleted file mode 100644 index 7a4cca0..0000000 --- a/examples/ptools API - Operations on Pathways.ipynb +++ /dev/null @@ -1,11390 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import os\n", - "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", - "\n", - "sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[u'|META|', u'|ECOLI|']\n" - ] - } - ], - "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways :all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways :all t ))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1347| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1347| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1474| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1474| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6690| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6690| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1348| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1348| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5162| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5162| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1352| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1352| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1505| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1505| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1355| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1355| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|2PHENDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|2PHENDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1465| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1465| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|TRESYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TRESYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PANTO-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PANTO-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1356| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1356| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1483| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1483| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1573| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1573| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1586| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1586| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUCONSUPER-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUCONSUPER-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1576| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1576| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLYCEROLMETAB-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYCEROLMETAB-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1512| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1512| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1577| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1577| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5123| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5123| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1313| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1313| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6387| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6387| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PYRIDNUCSAL-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDNUCSAL-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1578| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1578| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1490| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1490| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1581| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1581| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY3O-4106| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY3O-4106| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|KDOSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|KDOSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7761| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7761| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1582| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1582| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7971| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7971| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1534| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1534| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6952| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6952| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1518| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1518| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7184| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7184| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1584| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1584| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6038| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6038| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PYRIDNUCSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDNUCSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1585| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1585| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-981| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-981| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1495| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1495| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7181| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7181| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7801| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7801| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PYRUVDEHYD-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRUVDEHYD-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5509| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5509| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5350| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5350| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1559| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1559| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ALKANEMONOX-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ALKANEMONOX-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|HOMOSER-METSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HOMOSER-METSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6153| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6153| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1535| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1535| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7206| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7206| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|AST-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|AST-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5340| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5340| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-823| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-823| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-541| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-541| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|THREONINE-DEG2-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|THREONINE-DEG2-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5971| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5971| :sorted? t))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5436| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5436| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7197| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7197| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|THRDLCTCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|THRDLCTCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1533| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1533| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5437| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5437| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|TRNA-CHARGING-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TRNA-CHARGING-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|LCYSDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|LCYSDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6703| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6703| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1517| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1517| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLYCLEAV-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYCLEAV-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GALACTARDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTARDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7446| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7446| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7980| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7980| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ALADEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ALADEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|COA-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|COA-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|HOMOSERSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HOMOSERSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLYOXYLATE-BYPASS| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYOXYLATE-BYPASS| :sorted? 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t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7247| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7247| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1587| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1587| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUTORN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUTORN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1296| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1296| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6605| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6605| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6890| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6890| :sorted? t))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5668| :sorted? 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t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7193| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7193| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ALANINE-SYN2-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ALANINE-SYN2-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1317| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1317| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|LIPA-CORESYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|LIPA-CORESYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1470| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1470| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1315| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1315| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|SERSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SERSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1280| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1280| :sorted? t))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5698| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5698| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|FAO-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|FAO-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7344| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7344| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7187| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7187| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1503| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1503| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUAMCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUAMCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1264| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1264| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ASPARTATESYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ASPARTATESYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1221| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1221| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7343| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7343| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|NAGLIPASYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|NAGLIPASYN-PWY| :sorted? 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t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-66| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-66| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1493| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1493| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-521| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-521| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1334| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1334| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5965| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5965| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ASPARAGINE-BIOSYNTHESIS| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ASPARAGINE-BIOSYNTHESIS| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-4381| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-4381| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1335| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1335| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5686| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5686| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|MANNIDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|MANNIDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5659| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5659| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PPGPPMET-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PPGPPMET-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1550| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1550| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1353| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1353| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5966| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5966| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|HOMOSER-THRESYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HOMOSER-THRESYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1544| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1544| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|NONMEVIPP-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|NONMEVIPP-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1498| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1498| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1561| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1561| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUTSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUTSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1565| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1565| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1468| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1468| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1567| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1567| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUTSYNIII-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUTSYNIII-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1568| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1568| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1546| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1546| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|CYANCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|CYANCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|BGALACT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|BGALACT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1501| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1501| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|VALSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|VALSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1466| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1466| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-1269| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-1269| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GALACTITOLCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTITOLCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1481| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1481| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|IDNCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|IDNCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-4261| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-4261| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1182| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1182| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|HISTSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HISTSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|TREDEGLOW-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|TREDEGLOW-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-2161| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-2161| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|DTDPRHAMSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DTDPRHAMSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1506| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1506| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1306| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1306| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ACETOACETATE-DEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ACETOACETATE-DEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ENTNER-DOUDOROFF-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ENTNER-DOUDOROFF-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6614| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6614| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|DAPLYSINESYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DAPLYSINESYN-PWY| :sorted? t))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-pathway\n", - "(genes-of-pathway '|RHAMCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|RHAMCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|1CMET2-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|1CMET2-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1590| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1590| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7315| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7315| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLYCOGENSYNTH-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLYCOGENSYNTH-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GALACTCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|DARABCATK12-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|DARABCATK12-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1485| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1485| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1338| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1338| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6543| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6543| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|ARABCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|ARABCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-661| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-661| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1514| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1514| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7242| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7242| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-43| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-43| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1324| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1324| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GLUCONEO-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GLUCONEO-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|XYLCAT-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|XYLCAT-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-662| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-662| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|SORBDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SORBDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1303| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1303| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1492| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1492| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-301| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-301| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|GALACTMETAB-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|GALACTMETAB-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-5852| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-5852| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PLPSAL-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PLPSAL-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-321| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-321| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6608| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6608| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-4121| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-4121| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1519| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1519| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6961| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6961| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|SALVADEHYPOX-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|SALVADEHYPOX-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PYRIDOXSYN-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PYRIDOXSYN-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6617| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6617| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1591| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1591| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1497| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1497| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1507| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1507| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-6556| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-6556| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1588| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1588| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PROPIONMET-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PROPIONMET-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1295| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1295| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|RIBOSYN2-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|RIBOSYN2-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1597| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1597| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY-7195| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY-7195| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1458| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1458| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1321| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1321| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1500| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1500| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|HCAMHPDEG-PWY| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|HCAMHPDEG-PWY| :sorted? t))\n", - "genes-of-pathway\n", - "(genes-of-pathway '|PWY0-1336| :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-pathway '|PWY0-1336| :sorted? t))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|EG12082|',\n", - " u'|EG12088|',\n", - " u'|EG12090|',\n", - " u'|EG12091|',\n", - " u'|EG12092|',\n", - " u'|EG11773|',\n", - " u'|EG12093|',\n", - " u'|EG12089|',\n", - " u'|EG12087|',\n", - " u'|EG11774|',\n", - " u'|EG12086|',\n", - " u'|EG12084|',\n", - " u'|EG12083|',\n", - " u'|EG10330|',\n", - " u'|EG10331|',\n", - " u'|EG10332|',\n", - " u'|EG10333|']" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "sorted?\n", - "Keyword, Optional If true, the genes are sorted in the order in which the \n", - "corresponding reaction occurrs in the sequence of the pathway. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = 'all', base = True):\n", - " lst.append(ecoli.genes_of_pathway(pwy = pwy, sorted = True))\n", - "lst[-1]\n", - "\n", - "# sorted arg doesn't work because malformed key. sorted changed to sorted?" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1347| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1347| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1474| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1474| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-6690| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6690| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1348| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1348| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-5162| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-5162| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1352| :experimental-only? 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t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-7242| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-7242| :experimental-only? t :sorted? t))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-43| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-43| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1324| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1324| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|GLUCONEO-PWY| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|GLUCONEO-PWY| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|XYLCAT-PWY| :experimental-only? 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t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-301| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|GALACTMETAB-PWY| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|GALACTMETAB-PWY| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-5852| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-5852| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PLPSAL-PWY| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PLPSAL-PWY| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-321| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-321| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-6608| :experimental-only? 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t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PYRIDOXSYN-PWY| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-6617| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-6617| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1591| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1591| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1497| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1497| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1507| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1507| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-6556| :experimental-only? 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t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1597| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY-7195| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY-7195| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1458| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1458| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1321| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1321| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1500| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1500| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|HCAMHPDEG-PWY| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|HCAMHPDEG-PWY| :experimental-only? t :sorted? t))\n", - "enzymes-of-pathway\n", - "(enzymes-of-pathway '|PWY0-1336| :experimental-only? t :sorted? t)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-pathway '|PWY0-1336| :experimental-only? t :sorted? t))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|NADH-DHI-CPLX|', u'|FUMARATE-REDUCTASE|']" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "species\n", - "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", - "MetaCyc, only proteins found in those organisms will be returned. This list can \n", - "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", - "the documentation for the 'species slot‑unit for more information. \n", - "experimental-only?\n", - "Keyword, Optional When true, only return enzymes that have a non-computational \n", - "evidence code associated with it. \n", - "sorted?\n", - "Keyword, Optional If true, the enzymes are sorted in the order in which the \n", - "corresponding reaction occurrs in the sequence of the pathway. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.enzymes_of_pathway(pwy = pwy, sorted = True, experimental_only = True))\n", - "lst[-1]\n", - "\n", - "# same as previous function" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1347| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1474| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1474| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-6690| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6690| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1348| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1348| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-5162| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-5162| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1352| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1352| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1505| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1505| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1355| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1355| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|2PHENDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|2PHENDEG-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1465| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|TRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|TRESYN-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PANTO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PANTO-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1356| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1356| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1483| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1483| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1573| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1573| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1586| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1586| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|GLUCONSUPER-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|GLUCONSUPER-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1576| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1576| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|GLYCEROLMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|GLYCEROLMETAB-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1512| )\n", - 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"compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-662| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-662| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|SORBDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|SORBDEG-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1303| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1303| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1492| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1492| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-301| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-301| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|GALACTMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|GALACTMETAB-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-5852| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-5852| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PLPSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PLPSAL-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-321| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-321| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-6608| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6608| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-4121| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1519| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1519| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-6961| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6961| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|SALVADEHYPOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|SALVADEHYPOX-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PYRIDOXSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PYRIDOXSYN-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-6617| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6617| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1591| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1591| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1497| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1497| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1507| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1507| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-6556| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-6556| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1588| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1588| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PROPIONMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PROPIONMET-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1295| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1295| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|RIBOSYN2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|RIBOSYN2-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1597| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1597| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY-7195| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY-7195| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1458| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1458| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1321| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1321| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1500| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1500| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|HCAMHPDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|HCAMHPDEG-PWY| ))\n", - "compounds-of-pathway\n", - "(compounds-of-pathway '|PWY0-1336| )\n", - "(with-organism (:org-id '|ECOLI|) (compounds-of-pathway '|PWY0-1336| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|FUM|',\n", - " u'|SUC|',\n", - " u'|Menaquinones|',\n", - " u'|Menaquinols|',\n", - " u'|E-|',\n", - " u'|PROTON|',\n", - " u'|NAD|',\n", - " u'|NADH|']" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.compounds_of_pathway(pwy = pwy))\n", - "lst[-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1347| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1474| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1474| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6690| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6690| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1348| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1348| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-5162| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5162| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1352| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1352| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1505| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1505| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1355| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1355| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|2PHENDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|2PHENDEG-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1465| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|TRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|TRESYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PANTO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PANTO-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1356| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1356| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1483| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1483| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1573| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1573| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1586| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1586| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLUCONSUPER-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLUCONSUPER-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1576| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1576| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLYCEROLMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLYCEROLMETAB-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1512| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1512| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1577| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1577| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-5123| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5123| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1313| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1313| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6387| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6387| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PYRIDNUCSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRIDNUCSAL-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1578| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1578| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1490| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1490| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1581| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1581| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY3O-4106| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY3O-4106| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|KDOSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|KDOSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7761| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7761| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1582| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1582| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7971| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7971| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1534| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1534| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6952| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6952| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1518| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1518| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7184| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7184| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1584| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1584| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6038| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6038| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PYRIDNUCSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRIDNUCSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1585| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1585| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-981| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-981| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1495| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1495| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7181| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7181| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7801| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7801| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PYRUVDEHYD-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRUVDEHYD-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-5509| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5509| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-5350| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5350| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1559| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1559| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|ALKANEMONOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ALKANEMONOX-PWY| ))\n", - 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"substrates-of-pathway\n", - "(substrates-of-pathway '|HOMOSER-THRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|HOMOSER-THRESYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1544| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1544| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|NONMEVIPP-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|NONMEVIPP-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1498| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1498| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1561| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1561| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLUTSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLUTSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1565| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1565| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1468| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1468| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1567| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1567| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLUTSYNIII-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLUTSYNIII-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1568| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1568| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1546| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1546| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|CYANCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|CYANCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|BGALACT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|BGALACT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1501| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1501| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|VALSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|VALSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1466| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1466| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-1269| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-1269| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GALACTITOLCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GALACTITOLCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1481| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1481| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|IDNCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|IDNCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-4261| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-4261| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1182| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1182| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|HISTSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|HISTSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|TREDEGLOW-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|TREDEGLOW-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-2161| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-2161| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|DTDPRHAMSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|DTDPRHAMSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1506| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1506| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1306| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1306| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|ACETOACETATE-DEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ACETOACETATE-DEG-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|ENTNER-DOUDOROFF-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ENTNER-DOUDOROFF-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6614| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6614| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|DAPLYSINESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|DAPLYSINESYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|RHAMCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|RHAMCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|1CMET2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|1CMET2-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1590| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1590| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7315| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7315| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLYCOGENSYNTH-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLYCOGENSYNTH-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GALACTCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GALACTCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|DARABCATK12-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|DARABCATK12-PWY| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1485| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1485| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1338| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1338| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6543| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6543| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|ARABCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|ARABCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-661| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-661| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1514| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1514| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7242| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7242| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-43| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-43| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1324| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1324| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GLUCONEO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GLUCONEO-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|XYLCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|XYLCAT-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-662| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-662| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|SORBDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|SORBDEG-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1303| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1303| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1492| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1492| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-301| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-301| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|GALACTMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|GALACTMETAB-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-5852| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-5852| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PLPSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PLPSAL-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-321| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-321| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6608| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6608| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-4121| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1519| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1519| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6961| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6961| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|SALVADEHYPOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|SALVADEHYPOX-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PYRIDOXSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PYRIDOXSYN-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6617| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6617| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1591| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1591| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1497| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1497| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1507| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1507| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-6556| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-6556| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1588| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1588| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PROPIONMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PROPIONMET-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1295| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1295| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|RIBOSYN2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|RIBOSYN2-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1597| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1597| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY-7195| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY-7195| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1458| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1458| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1321| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1321| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1500| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1500| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|HCAMHPDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|HCAMHPDEG-PWY| ))\n", - "substrates-of-pathway\n", - "(substrates-of-pathway '|PWY0-1336| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-pathway '|PWY0-1336| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|NADH|',\n", - " u'|Menaquinones|',\n", - " u'|Menaquinols|',\n", - " u'|PROTON|',\n", - " u'|TRIMETHYLAMINE-N-O|'],\n", - " [u'|TRIMETHYLAMINE-N-O|', u'|NADH|'],\n", - " [u'|NAD|',\n", - " u'|Menaquinols|',\n", - " u'|PROTON|',\n", - " u'|TRIMETHYLAMINE|',\n", - " u'|WATER|',\n", - " u'|Menaquinones|'],\n", - " [u'|WATER|', u'|TRIMETHYLAMINE|', u'|NAD|']]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.substrates_of_pathway(pwy = pwy))\n", - "lst[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1347| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1474| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1474| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6690| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6690| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1348| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1348| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5162| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5162| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1352| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1352| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1505| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1505| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1355| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1355| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|2PHENDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|2PHENDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1465| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|TRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TRESYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PANTO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PANTO-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1356| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1356| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ETOH-ACETYLCOA-ANA-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1483| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1483| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1573| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1573| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1586| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1586| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLUCONSUPER-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUCONSUPER-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1576| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1576| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLYCEROLMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCEROLMETAB-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1512| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1512| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1577| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1577| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5123| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5123| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1313| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1313| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6387| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6387| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PYRIDNUCSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDNUCSAL-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1578| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1578| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1490| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1490| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1581| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1581| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY3O-4106| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY3O-4106| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|KDOSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|KDOSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7761| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7761| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1582| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1582| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7971| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7971| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1534| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1534| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6952| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6952| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1518| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1518| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7184| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7184| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1584| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1584| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6038| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6038| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PYRIDNUCSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDNUCSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1585| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1585| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-981| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-981| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1495| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1495| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7181| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7181| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7801| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7801| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PYRUVDEHYD-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRUVDEHYD-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5509| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5509| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5350| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5350| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1559| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1559| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ALKANEMONOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ALKANEMONOX-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|HOMOSER-METSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HOMOSER-METSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6153| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6153| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1535| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1535| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7206| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7206| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|AST-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|AST-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5340| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5340| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-823| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-823| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-541| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-541| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|THREONINE-DEG2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|THREONINE-DEG2-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5971| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5971| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5436| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5436| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7197| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7197| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|THRDLCTCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|THRDLCTCAT-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1533| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1533| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5437| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5437| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|TRNA-CHARGING-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TRNA-CHARGING-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|LCYSDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|LCYSDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6703| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6703| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1517| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1517| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLYCLEAV-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCLEAV-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GALACTARDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTARDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7446| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7446| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7980| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7980| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ALADEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ALADEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|COA-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|COA-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|HOMOSERSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HOMOSERSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLYOXYLATE-BYPASS| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYOXYLATE-BYPASS| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|SERDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SERDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6163| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6163| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLUTAMINDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUTAMINDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-501| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-501| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-461| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-461| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PROUT-PWY-I| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PROUT-PWY-I| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1275| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1275| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5901| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5901| ))\n", - 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"variants-of-pathway\n", - "(variants-of-pathway '|TREDEGLOW-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|TREDEGLOW-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-2161| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-2161| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|DTDPRHAMSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DTDPRHAMSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1506| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1506| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1306| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1306| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ACETOACETATE-DEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ACETOACETATE-DEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ENTNER-DOUDOROFF-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ENTNER-DOUDOROFF-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6614| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6614| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|DAPLYSINESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DAPLYSINESYN-PWY| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "variants-of-pathway\n", - "(variants-of-pathway '|RHAMCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|RHAMCAT-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|1CMET2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|1CMET2-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1590| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1590| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7315| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7315| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLYCOGENSYNTH-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLYCOGENSYNTH-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GALACTCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTCAT-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|DARABCATK12-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|DARABCATK12-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1485| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1485| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1338| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1338| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6543| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6543| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|ARABCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|ARABCAT-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-661| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-661| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1514| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1514| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7242| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7242| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-43| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-43| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1324| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1324| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GLUCONEO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GLUCONEO-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|XYLCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|XYLCAT-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-662| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-662| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|SORBDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SORBDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1303| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1303| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1492| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1492| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-301| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-301| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|GALACTMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|GALACTMETAB-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-5852| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-5852| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PLPSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PLPSAL-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-321| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-321| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6608| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6608| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-4121| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1519| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1519| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6961| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6961| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|SALVADEHYPOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|SALVADEHYPOX-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PYRIDOXSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PYRIDOXSYN-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6617| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6617| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1591| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1591| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1497| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1497| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1507| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1507| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-6556| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-6556| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1588| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1588| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PROPIONMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PROPIONMET-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1295| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1295| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|RIBOSYN2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|RIBOSYN2-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1597| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1597| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY-7195| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY-7195| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1458| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1458| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1321| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1321| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1500| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1500| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|HCAMHPDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|HCAMHPDEG-PWY| ))\n", - "variants-of-pathway\n", - "(variants-of-pathway '|PWY0-1336| )\n", - "(with-organism (:org-id '|ECOLI|) (variants-of-pathway '|PWY0-1336| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[],\n", - " [u'|PWY-7195|', u'|PWY-6556|'],\n", - " [u'|PWY0-1597|'],\n", - " [u'|RIBOSYN2-PWY|'],\n", - " [u'|PWY0-1295|', u'|PWY-6556|'],\n", - " [],\n", - " [u'|PWY0-1584|', u'|PWY0-1581|', u'|PWY0-1573|', u'|PWY0-1352|'],\n", - " [],\n", - " [],\n", - " []]" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.variants_of_pathway(pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1347| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1474| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1474| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6690| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6690| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1348| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1348| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-5162| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5162| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1352| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1352| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1505| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1505| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1355| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1355| ))\n", - "pathway-components\n", - "(pathway-components '|2PHENDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|2PHENDEG-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1465| ))\n", - "pathway-components\n", - "(pathway-components '|TRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|TRESYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PANTO-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PANTO-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1356| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1356| ))\n", - "pathway-components\n", - "(pathway-components '|ETOH-ACETYLCOA-ANA-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|ETOH-ACETYLCOA-ANA-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1483| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1483| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1573| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1573| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1586| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1586| ))\n", - "pathway-components\n", - "(pathway-components '|GLUCONSUPER-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLUCONSUPER-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1576| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1576| ))\n", - "pathway-components\n", - "(pathway-components '|GLYCEROLMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLYCEROLMETAB-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1512| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1512| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1577| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1577| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-5123| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5123| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1313| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1313| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6387| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6387| ))\n", - "pathway-components\n", - "(pathway-components '|PYRIDNUCSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PYRIDNUCSAL-PWY| ))\n", - 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"pathway-components\n", - "(pathway-components '|MANNIDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|MANNIDEG-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-5659| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5659| ))\n", - "pathway-components\n", - "(pathway-components '|PPGPPMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PPGPPMET-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1550| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1550| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1353| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1353| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-5966| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5966| ))\n", - "pathway-components\n", - "(pathway-components '|HOMOSER-THRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|HOMOSER-THRESYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1544| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1544| ))\n", - "pathway-components\n", - "(pathway-components '|NONMEVIPP-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|NONMEVIPP-PWY| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "pathway-components\n", - "(pathway-components '|PWY0-1498| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1498| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1561| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1561| ))\n", - "pathway-components\n", - "(pathway-components '|GLUTSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLUTSYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1565| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1565| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1468| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1468| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1567| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1567| ))\n", - "pathway-components\n", - "(pathway-components '|GLUTSYNIII-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GLUTSYNIII-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1568| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1568| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1546| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1546| ))\n", - "pathway-components\n", - "(pathway-components '|CYANCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|CYANCAT-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|BGALACT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|BGALACT-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1501| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1501| ))\n", - "pathway-components\n", - "(pathway-components '|VALSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|VALSYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1466| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1466| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-1269| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-1269| ))\n", - "pathway-components\n", - "(pathway-components '|GALACTITOLCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GALACTITOLCAT-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1481| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1481| ))\n", - "pathway-components\n", - "(pathway-components '|IDNCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|IDNCAT-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-4261| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-4261| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1182| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1182| ))\n", - "pathway-components\n", - "(pathway-components '|HISTSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|HISTSYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|TREDEGLOW-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|TREDEGLOW-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-2161| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-2161| ))\n", - "pathway-components\n", - "(pathway-components '|DTDPRHAMSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|DTDPRHAMSYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1506| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1506| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1306| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1306| ))\n", - "pathway-components\n", - "(pathway-components '|ACETOACETATE-DEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|ACETOACETATE-DEG-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|ENTNER-DOUDOROFF-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|ENTNER-DOUDOROFF-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6614| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6614| ))\n", - "pathway-components\n", - "(pathway-components '|DAPLYSINESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|DAPLYSINESYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|RHAMCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|RHAMCAT-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|1CMET2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|1CMET2-PWY| ))\n", - 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"pathway-components\n", - "(pathway-components '|GALACTMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|GALACTMETAB-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-5852| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-5852| ))\n", - "pathway-components\n", - "(pathway-components '|PLPSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PLPSAL-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-321| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-321| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6608| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6608| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-4121| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1519| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1519| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6961| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6961| ))\n", - "pathway-components\n", - "(pathway-components '|SALVADEHYPOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|SALVADEHYPOX-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PYRIDOXSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PYRIDOXSYN-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6617| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6617| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1591| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1591| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1497| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1497| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1507| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1507| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-6556| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-6556| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1588| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1588| ))\n", - "pathway-components\n", - "(pathway-components '|PROPIONMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PROPIONMET-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1295| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1295| ))\n", - "pathway-components\n", - "(pathway-components '|RIBOSYN2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|RIBOSYN2-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1597| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1597| ))\n", - "pathway-components\n", - "(pathway-components '|PWY-7195| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY-7195| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1458| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1458| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1321| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1321| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1500| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1500| ))\n", - "pathway-components\n", - "(pathway-components '|HCAMHPDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|HCAMHPDEG-PWY| ))\n", - "pathway-components\n", - "(pathway-components '|PWY0-1336| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-components '|PWY0-1336| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[[u'|RXN0-5264|', u'|RXN0-5388|']], 1, 2, 2]" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|, which is not a super-pathway (i.e., does \n", - "not have any entries in its 'sub‑pathways slot). \n", - "rxn-list\n", - "Optional The list of reactions to use as the starting list of connected \n", - "component clusters. Defaults to (get‑slot‑values pwy 'reaction‑list).\n", - "\n", - "pred-list\n", - "Optional The list of reaction predecessors to iterate from in order to cluster \n", - "the reactions in rxn‑list. Defaults to (get‑slot‑values pwy 'predecessors).\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.pathway_components(pwy = pwy))\n", - "lst[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1347| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1474| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1474| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6690| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6690| ))\n", - "noncontiguous-pathway-p\n", - 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"(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6121| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|TYRSYN| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|TYRSYN| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-862| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-862| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|TCA| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|TCA| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6122| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6122| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1305| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1305| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GLUCOSE1PMETAB-PWY| )\n", - 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"(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1021| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1301| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1301| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-44| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-44| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-163| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-163| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|NRI-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|NRI-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-42| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-42| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1569| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1569| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|LYXMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|LYXMET-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ALANINE-VALINESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ALANINE-VALINESYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1300| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1300| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1499| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1499| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1314| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1314| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1527| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1527| ))\n", - "noncontiguous-pathway-p\n", - 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"(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7187| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1503| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1503| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GLUAMCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLUAMCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1264| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1264| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ASPARTATESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ASPARTATESYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1221| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1221| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7343| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7343| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|NAGLIPASYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|NAGLIPASYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1482| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1482| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PUTDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PUTDEG-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|TRPSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|TRPSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|CARNMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|CARNMET-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7335| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7335| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5837| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5837| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|KDO-LIPASYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|KDO-LIPASYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1509| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1509| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GLNSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLNSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1471| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1471| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7346| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7346| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6708| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6708| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1487| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1487| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5084| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5084| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1261| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1261| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ILEUSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ILEUSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7544| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7544| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1241| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1241| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|UDPNAGSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|UDPNAGSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|MENAQUINONESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|MENAQUINONESYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1515| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1515| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7545| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7545| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ASPARAGINESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ASPARAGINESYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|FASYN-ELONG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|FASYN-ELONG-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1329| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1329| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6123| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6123| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-66| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-66| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1493| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1493| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-521| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-521| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1334| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1334| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5965| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5965| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ASPARAGINE-BIOSYNTHESIS| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ASPARAGINE-BIOSYNTHESIS| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-4381| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-4381| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1335| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1335| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5686| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5686| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|MANNIDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|MANNIDEG-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5659| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5659| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PPGPPMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PPGPPMET-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1550| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1550| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1353| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1353| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5966| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5966| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|HOMOSER-THRESYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|HOMOSER-THRESYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1544| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1544| ))\n", - "noncontiguous-pathway-p\n", - 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"(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1567| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GLUTSYNIII-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLUTSYNIII-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1568| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1568| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1546| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1546| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|CYANCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|CYANCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|BGALACT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|BGALACT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1501| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1501| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|VALSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|VALSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1466| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1466| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-1269| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-1269| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GALACTITOLCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTITOLCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1481| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1481| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|IDNCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|IDNCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-4261| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-4261| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1182| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1182| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|HISTSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|HISTSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|TREDEGLOW-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|TREDEGLOW-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-2161| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-2161| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|DTDPRHAMSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|DTDPRHAMSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - 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"(noncontiguous-pathway-p '|RHAMCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|RHAMCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|1CMET2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|1CMET2-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1590| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1590| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7315| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7315| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GLYCOGENSYNTH-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GLYCOGENSYNTH-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GALACTCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|DARABCATK12-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|DARABCATK12-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1485| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1485| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1338| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1338| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6543| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6543| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|ARABCAT-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|ARABCAT-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-661| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-661| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1514| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1514| ))\n", - 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"(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|SORBDEG-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1303| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1303| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1492| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1492| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-301| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-301| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|GALACTMETAB-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|GALACTMETAB-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-5852| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-5852| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PLPSAL-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PLPSAL-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-321| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-321| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6608| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6608| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-4121| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-4121| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1519| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1519| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6961| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6961| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|SALVADEHYPOX-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|SALVADEHYPOX-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PYRIDOXSYN-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PYRIDOXSYN-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6617| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6617| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1591| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1591| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1497| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1497| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1507| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1507| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-6556| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-6556| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1588| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1588| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PROPIONMET-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PROPIONMET-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1295| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1295| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|RIBOSYN2-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|RIBOSYN2-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1597| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1597| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY-7195| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY-7195| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1458| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1458| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1321| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1321| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1500| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1500| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|HCAMHPDEG-PWY| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|HCAMHPDEG-PWY| ))\n", - "noncontiguous-pathway-p\n", - "(noncontiguous-pathway-p '|PWY0-1336| )\n", - "(with-organism (:org-id '|ECOLI|) (noncontiguous-pathway-p '|PWY0-1336| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[False, False, False, False, False, True, False, True, False, False]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.noncontiguous_pathway_p(pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-pathways\n", - "(all-pathways ::all t )\n", - "(with-organism (:org-id '|ECOLI|) (all-pathways ::all t ))\n", - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN-15348| '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|RXN-15348| '|PWY0-1347| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN-15348| '|LACTALDREDUCT-RXN| '|PWY0-1347| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN-15348| '|LACTALDREDUCT-RXN| '|PWY0-1347| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN-15348| '|PFLDEACTIV-RXN| '|PWY0-1347| )\n", - 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"(rxns-adjacent-in-pwy-p '|RXN0-1137| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7298| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-7298| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-1137| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|RXN0-1137| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|BADH-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|BADH-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|RXN0-1137| '|DMKCYT-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|RXN0-1137| '|DMKCYT-RXN| '|PWY0-1465| ))\n", - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN-15348| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN-15348| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7094| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7094| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-7298| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|RXN0-1137| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|BADH-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|BADH-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|BADH-RXN| '|DMKCYT-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|BADH-RXN| '|DMKCYT-RXN| '|PWY0-1465| ))\n", - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN-15348| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN-15348| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|LACTALDREDUCT-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|PFLDEACTIV-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|OHMETPYRKIN-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7094| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7094| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|TRIOSEPISOMERIZATION-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7298| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-7298| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-1137| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|RXN0-1137| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|BADH-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|BADH-RXN| '|PWY0-1465| ))\n", - "rxns-adjacent-in-pwy-p\n", - "(rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|DMKCYT-RXN| '|PWY0-1465| )\n", - "(with-organism (:org-id '|ECOLI|) (rxns-adjacent-in-pwy-p '|DMKCYT-RXN| '|DMKCYT-RXN| '|PWY0-1465| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|DMKCYT-RXN|', u'|RXN-15348|', False],\n", - " [u'|DMKCYT-RXN|', u'|LACTALDREDUCT-RXN|', False],\n", - " [u'|DMKCYT-RXN|', u'|PFLDEACTIV-RXN|', False],\n", - " [u'|DMKCYT-RXN|', u'|OHMETPYRKIN-RXN|', False],\n", - " [u'|DMKCYT-RXN|', u'|RXN0-7094|', False],\n", - " [u'|DMKCYT-RXN|', u'|TRIOSEPISOMERIZATION-RXN|', False],\n", - " [u'|DMKCYT-RXN|', u'|RXN0-7298|', False],\n", - " [u'|DMKCYT-RXN|', u'|RXN0-1137|', False],\n", - " [u'|DMKCYT-RXN|', u'|BADH-RXN|', False],\n", - " [u'|DMKCYT-RXN|', u'|DMKCYT-RXN|', False]]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn1\n", - "An instance of the class |Reactions|. \n", - "rxn2\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True)[0:10]:\n", - " for rxn1 in ecoli.all_rxns(rxn_type = ':all')[0:10]:\n", - " for rxn2 in ecoli.all_rxns(rxn_type = ':all')[0:10]:\n", - " lst.append([rxn1, rxn2, ecoli.rxns_adjacent_in_pwy_p(rxn1 = rxn1, rxn2 = rxn2, pwy = pwy)])\n", - "# lst.append(ecoli.rxns_adjacent_in_pwy_p(rxn1 = u'|RXN0-5264|', rxn2 = u'|RXN0-5388|', pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb b/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb deleted file mode 100644 index a93af8b..0000000 --- a/examples/ptools API - Operations on Proteins and Protein Complexes.ipynb +++ /dev/null @@ -1,1277 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import os\n", - "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", - "\n", - "sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[u'|META|', u'|ECOLI|']\n", - "class-name-p\n", - "(class-name-p \"proteins\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"proteins\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Proteins| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Proteins| ))\n", - "get-class\n", - "(get-class |Proteins| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Proteins| ))\n", - "all-protein-complexes\n", - "(all-protein-complexes :filter :all)\n", - "(with-organism (:org-id '|ECOLI|) (all-protein-complexes :filter :all))\n" - ] - } - ], - "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", - "complexes = ecoli.all_protein_complexes()[0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "monomers-of-protein\n", - "(monomers-of-protein '|CPLX0-7660| :coefficients? t :unmodify? t)\n", - "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|CPLX0-7660| :coefficients? t :unmodify? t))\n", - "monomers-of-protein\n", - "(monomers-of-protein '|CPLX0-8247| :coefficients? t :unmodify? t)\n", - "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|CPLX0-8247| :coefficients? t :unmodify? t))\n", - "[[[u'|G6106-MONOMER|'], [4]], [[u'|URAA-MONOMER|'], [2]]]\n", - "monomers-of-protein\n", - "(monomers-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|OPPC-MONOMER| ))\n", - "monomers-of-protein\n", - "(monomers-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (monomers-of-protein '|YHBN-MONOMER| ))\n", - "[[[u'|OPPC-MONOMER|'], [1]], [[u'|YHBN-MONOMER|'], [1]]]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "coefficients?\n", - "Keyword, Optional If true, then the second return value of the function will be \n", - "a list of monomer coefficients. Defaults to true. \n", - "unmodify?\n", - "Keyword, Optional If true, obtain the monomers of the unmodified form of p.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.monomers_of_protein(protein = protein, coefficients = True, unmodify = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.monomers_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "base-components-of-protein\n", - "(base-components-of-protein '|CPLX0-7660| :exclude-small-molecules? t)\n", - "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|CPLX0-7660| :exclude-small-molecules? t))\n", - "base-components-of-protein\n", - "(base-components-of-protein '|CPLX0-8247| :exclude-small-molecules? t)\n", - "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|CPLX0-8247| :exclude-small-molecules? t))\n", - "[[[u'|G6106-MONOMER|'], [4]], [[u'|URAA-MONOMER|'], [2]]]\n", - "base-components-of-protein\n", - "(base-components-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|OPPC-MONOMER| ))\n", - "base-components-of-protein\n", - "(base-components-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (base-components-of-protein '|YHBN-MONOMER| ))\n", - "[[[u'|OPPC-MONOMER|'], [1]], [[u'|YHBN-MONOMER|'], [1]]]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "exclude-small-molecules?\n", - "Keyword, Optional If nil, then small molecule components are also returned. \n", - "Default value is true. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.base_components_of_protein(protein = protein, exclude_small_molecules = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.base_components_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "containers-of\n", - "(containers-of '|CPLX0-7660| t )\n", - "(with-organism (:org-id '|ECOLI|) (containers-of '|CPLX0-7660| t ))\n", - "containers-of\n", - "(containers-of '|CPLX0-8247| t )\n", - "(with-organism (:org-id '|ECOLI|) (containers-of '|CPLX0-8247| t ))\n", - "[[], []]\n", - "containers-of\n", - "(containers-of '|OPPC-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (containers-of '|OPPC-MONOMER| nil ))\n", - "containers-of\n", - "(containers-of '|YHBN-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (containers-of '|YHBN-MONOMER| nil ))\n", - "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.containers_of(protein = protein, exclude_self = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "protein-or-rna-containers-of\n", - "(protein-or-rna-containers-of '|CPLX0-7660| nil )\n", - "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|CPLX0-7660| nil ))\n", - "protein-or-rna-containers-of\n", - "(protein-or-rna-containers-of '|CPLX0-8247| nil )\n", - "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|CPLX0-8247| nil ))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "protein-or-rna-containers-of\n", - "(protein-or-rna-containers-of '|OPPC-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|OPPC-MONOMER| nil ))\n", - "protein-or-rna-containers-of\n", - "(protein-or-rna-containers-of '|YHBN-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (protein-or-rna-containers-of '|YHBN-MONOMER| nil ))\n", - "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "homomultimeric-containers-of\n", - "(homomultimeric-containers-of '|CPLX0-7660| nil )\n", - "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|CPLX0-7660| nil ))\n", - "homomultimeric-containers-of\n", - "(homomultimeric-containers-of '|CPLX0-8247| nil )\n", - "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|CPLX0-8247| nil ))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "homomultimeric-containers-of\n", - "(homomultimeric-containers-of '|OPPC-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|OPPC-MONOMER| nil ))\n", - "homomultimeric-containers-of\n", - "(homomultimeric-containers-of '|YHBN-MONOMER| nil )\n", - "(with-organism (:org-id '|ECOLI|) (homomultimeric-containers-of '|YHBN-MONOMER| nil ))\n", - "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "polypeptide-or-homomultimer-p\n", - "(polypeptide-or-homomultimer-p '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|CPLX0-7660| ))\n", - "polypeptide-or-homomultimer-p\n", - "(polypeptide-or-homomultimer-p '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|CPLX0-8247| ))\n", - "[True, True]\n", - "polypeptide-or-homomultimer-p\n", - "(polypeptide-or-homomultimer-p '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|OPPC-MONOMER| ))\n", - "polypeptide-or-homomultimer-p\n", - "(polypeptide-or-homomultimer-p '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (polypeptide-or-homomultimer-p '|YHBN-MONOMER| ))\n", - "[True, True]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "unmodified-form\n", - "(unmodified-form '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-form '|CPLX0-7660| ))\n", - "unmodified-form\n", - "(unmodified-form '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-form '|CPLX0-8247| ))\n", - "[u'|CPLX0-7660|', u'|CPLX0-8247|']\n", - "unmodified-form\n", - "(unmodified-form '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-form '|OPPC-MONOMER| ))\n", - "unmodified-form\n", - "(unmodified-form '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-form '|YHBN-MONOMER| ))\n", - "[u'|OPPC-MONOMER|', u'|YHBN-MONOMER|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.unmodified_form(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.unmodified_form(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "unmodified-or-unbound-form\n", - "(unmodified-or-unbound-form '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|CPLX0-7660| ))\n", - "unmodified-or-unbound-form\n", - "(unmodified-or-unbound-form '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|CPLX0-8247| ))\n", - "[u'|CPLX0-7660|', u'|CPLX0-8247|']\n", - "unmodified-or-unbound-form\n", - "(unmodified-or-unbound-form '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|OPPC-MONOMER| ))\n", - "unmodified-or-unbound-form\n", - "(unmodified-or-unbound-form '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (unmodified-or-unbound-form '|YHBN-MONOMER| ))\n", - "[u'|OPPC-MONOMER|', u'|YHBN-MONOMER|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "reduce-modified-proteins\n", - "(reduce-modified-proteins '(|CPLX0-7660|) :debind? t)\n", - "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|CPLX0-7660|) :debind? t))\n", - "reduce-modified-proteins\n", - "(reduce-modified-proteins '(|CPLX0-8247|) :debind? t)\n", - "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|CPLX0-8247|) :debind? t))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "reduce-modified-proteins\n", - "(reduce-modified-proteins '(|OPPC-MONOMER|) )\n", - "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|OPPC-MONOMER|) ))\n", - "reduce-modified-proteins\n", - "(reduce-modified-proteins '(|YHBN-MONOMER|) )\n", - "(with-organism (:org-id '|ECOLI|) (reduce-modified-proteins '(|YHBN-MONOMER|) ))\n", - "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "prots\n", - "A list of instances of the class |Proteins|. \n", - "debind?\n", - "Keyword, Optional When non-nil, the proteins are further simplified by obtaining \n", - "the unbound form of the protein, if it is bound to a small molecule. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reduce_modified_proteins(prots = [protein], debind = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reduce_modified_proteins(prots = [protein]))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-direct-forms-of-protein\n", - "(all-direct-forms-of-protein '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|CPLX0-7660| ))\n", - "all-direct-forms-of-protein\n", - "(all-direct-forms-of-protein '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|CPLX0-8247| ))\n", - "[[u'|G6106-MONOMER|', u'|CPLX0-7660|'], [u'|URAA-MONOMER|', u'|CPLX0-8247|']]\n", - "all-direct-forms-of-protein\n", - "(all-direct-forms-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|OPPC-MONOMER| ))\n", - "all-direct-forms-of-protein\n", - "(all-direct-forms-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (all-direct-forms-of-protein '|YHBN-MONOMER| ))\n", - "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-forms-of-protein\n", - "(all-forms-of-protein '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|CPLX0-7660| ))\n", - "all-forms-of-protein\n", - "(all-forms-of-protein '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|CPLX0-8247| ))\n", - "[[u'|G6106-MONOMER|', u'|CPLX0-7660|'], [u'|URAA-MONOMER|', u'|CPLX0-8247|']]\n", - "all-forms-of-protein\n", - "(all-forms-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|OPPC-MONOMER| ))\n", - "all-forms-of-protein\n", - "(all-forms-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (all-forms-of-protein '|YHBN-MONOMER| ))\n", - "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "modified-forms\n", - "(modified-forms '|CPLX0-7660| t t )\n", - "(with-organism (:org-id '|ECOLI|) (modified-forms '|CPLX0-7660| t t ))\n", - "modified-forms\n", - "(modified-forms '|CPLX0-8247| t t )\n", - "(with-organism (:org-id '|ECOLI|) (modified-forms '|CPLX0-8247| t t ))\n", - "[[], []]\n", - "modified-forms\n", - "(modified-forms '|OPPC-MONOMER| nil nil )\n", - "(with-organism (:org-id '|ECOLI|) (modified-forms '|OPPC-MONOMER| nil nil ))\n", - "modified-forms\n", - "(modified-forms '|YHBN-MONOMER| nil nil )\n", - "(with-organism (:org-id '|ECOLI|) (modified-forms '|YHBN-MONOMER| nil nil ))\n", - "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_forms(protein = protein, all_variants = True, exclude_self= True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_forms(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "modified-and-unmodified-forms\n", - "(modified-and-unmodified-forms '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|CPLX0-7660| ))\n", - "modified-and-unmodified-forms\n", - "(modified-and-unmodified-forms '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|CPLX0-8247| ))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "modified-and-unmodified-forms\n", - "(modified-and-unmodified-forms '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|OPPC-MONOMER| ))\n", - "modified-and-unmodified-forms\n", - "(modified-and-unmodified-forms '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-and-unmodified-forms '|YHBN-MONOMER| ))\n", - "[[u'|OPPC-MONOMER|'], [u'|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "modified-containers\n", - "(modified-containers '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-containers '|CPLX0-7660| ))\n", - "modified-containers\n", - "(modified-containers '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-containers '|CPLX0-8247| ))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "modified-containers\n", - "(modified-containers '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-containers '|OPPC-MONOMER| ))\n", - "modified-containers\n", - "(modified-containers '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (modified-containers '|YHBN-MONOMER| ))\n", - "[[u'|OPPC-MONOMER|', u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|YHBN-MONOMER|', u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_containers(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_containers(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "top-containers\n", - "(top-containers '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (top-containers '|CPLX0-7660| ))\n", - "top-containers\n", - "(top-containers '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (top-containers '|CPLX0-8247| ))\n", - "[[u'|CPLX0-7660|'], [u'|CPLX0-8247|']]\n", - "top-containers\n", - "(top-containers '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (top-containers '|OPPC-MONOMER| ))\n", - "top-containers\n", - "(top-containers '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (top-containers '|YHBN-MONOMER| ))\n", - "[[u'|CPLX0-3970|', u'|ABC-22-CPLX|'], [u'|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.top_containers(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.top_containers(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "small-molecule-cplxes-of-prot\n", - "(small-molecule-cplxes-of-prot '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|CPLX0-7660| ))\n", - "small-molecule-cplxes-of-prot\n", - "(small-molecule-cplxes-of-prot '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|CPLX0-8247| ))\n", - "[[], []]\n", - "small-molecule-cplxes-of-prot\n", - "(small-molecule-cplxes-of-prot '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|OPPC-MONOMER| ))\n", - "small-molecule-cplxes-of-prot\n", - "(small-molecule-cplxes-of-prot '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (small-molecule-cplxes-of-prot '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-protein\n", - "(genes-of-protein '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|CPLX0-7660| ))\n", - "genes-of-protein\n", - "(genes-of-protein '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|CPLX0-8247| ))\n", - "[[u'|G6106|'], [u'|EG12129|']]\n", - "genes-of-protein\n", - "(genes-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|OPPC-MONOMER| ))\n", - "genes-of-protein\n", - "(genes-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-protein '|YHBN-MONOMER| ))\n", - "[[u'|EG10676|'], [u'|G7665|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.genes_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-of-proteins\n", - "(genes-of-proteins '(|CPLX0-7660|) )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|CPLX0-7660|) ))\n", - "genes-of-proteins\n", - "(genes-of-proteins '(|CPLX0-8247|) )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|CPLX0-8247|) ))\n", - "[[u'|G6106|'], [u'|EG12129|']]\n", - "genes-of-proteins\n", - "(genes-of-proteins '(|OPPC-MONOMER|) )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|OPPC-MONOMER|) ))\n", - "genes-of-proteins\n", - "(genes-of-proteins '(|YHBN-MONOMER|) )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-proteins '(|YHBN-MONOMER|) ))\n", - "[[u'|EG10676|'], [u'|G7665|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.genes_of_proteins(prots = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_of_proteins(prots = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "reactions-of-enzyme\n", - "(reactions-of-enzyme '|CPLX0-7660| :include-subreactions? t)\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|CPLX0-7660| :include-subreactions? t))\n", - "reactions-of-enzyme\n", - "(reactions-of-enzyme '|CPLX0-8247| :include-subreactions? t)\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|CPLX0-8247| :include-subreactions? t))\n", - "[[u'|RXN0-4301|'], [u'|TRANS-RXN-132|']]\n", - "reactions-of-enzyme\n", - "(reactions-of-enzyme '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|OPPC-MONOMER| ))\n", - "reactions-of-enzyme\n", - "(reactions-of-enzyme '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-enzyme '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "kb\n", - "Keyword, Optional The KB object of the KB in which to find the associated \n", - "reactions. Defaults to the current PGDB. \n", - "include-specific-forms?\n", - "Keyword, Optional When true, specific forms of associated generic reactions are \n", - "also returned. Default value is true. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reactions_of_enzyme(protein = protein, include_subreactions = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reactions_of_enzyme(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "species-of-protein\n", - "(species-of-protein '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (species-of-protein '|CPLX0-7660| ))\n", - "species-of-protein\n", - "(species-of-protein '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (species-of-protein '|CPLX0-8247| ))\n", - "[[u'|ECOLI|'], [u'|ECOLI|']]\n", - "species-of-protein\n", - "(species-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (species-of-protein '|OPPC-MONOMER| ))\n", - "species-of-protein\n", - "(species-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (species-of-protein '|YHBN-MONOMER| ))\n", - "[[u'|ECOLI|'], [u'|ECOLI|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.species_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.species_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzyme-p\n", - "(enzyme-p '|CPLX0-7660| :any )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-p '|CPLX0-7660| :any ))\n", - "enzyme-p\n", - "(enzyme-p '|CPLX0-8247| :any )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-p '|CPLX0-8247| :any ))\n", - "[True, True]\n", - "enzyme-p\n", - "(enzyme-p '|OPPC-MONOMER| :non-transport-non-pathway )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-p '|OPPC-MONOMER| :non-transport-non-pathway ))\n", - "enzyme-p\n", - "(enzyme-p '|YHBN-MONOMER| :non-transport-non-pathway )\n", - "(with-organism (:org-id '|ECOLI|) (enzyme-p '|YHBN-MONOMER| :non-transport-non-pathway ))\n", - "[False, False]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "type\n", - "Optional Can take on one of the following values to select more precisely what \n", - "is meant by an “enzyme”:\n", - "\n", - ":any\n", - "Any protein that catalyzes a reaction is considered an enzyme. \n", - ":chemical-change\n", - "If the reactants and products of the catalyzed reactin differ, and not just by \n", - "their cellular location, then the protein is considered an enzyme. \n", - ":small-molecule\n", - "If the reactants of the catalyzed reaction differ and are small molecules, then \n", - "the protein is considered an enzyme. \n", - ":transport\n", - "If the protein catalyzes a transport reaction. \n", - ":non-transport\n", - "If the protein only catalyzes non-transport reactions. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'any'))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'non-transport-non-pathway'))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "leader-peptide?\n", - "(leader-peptide? '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (leader-peptide? '|CPLX0-7660| ))\n" - ] - } - ], - "source": [ - "try:\n", - " lst = []\n", - " for protein in complexes:\n", - " lst.append(ecoli.leader_peptide_p(protein = protein))\n", - " print(lst[-10:])\n", - "\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.leader_peptide_p(protein = protein))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "protein-p\n", - "(protein-p '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (protein-p '|CPLX0-7660| ))\n", - "protein-p\n", - "(protein-p '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (protein-p '|CPLX0-8247| ))\n", - "[u'|Proteins|', u'|Proteins|']\n", - "protein-p\n", - "(protein-p '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (protein-p '|OPPC-MONOMER| ))\n", - "protein-p\n", - "(protein-p '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (protein-p '|YHBN-MONOMER| ))\n", - "[u'|Proteins|', u'|Proteins|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_p(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_p(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "complex-p\n", - "(complex-p '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (complex-p '|CPLX0-7660| ))\n", - "complex-p\n", - "(complex-p '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (complex-p '|CPLX0-8247| ))\n", - "[u'|Protein-Complexes|', u'|Protein-Complexes|']\n", - "complex-p\n", - "(complex-p '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (complex-p '|OPPC-MONOMER| ))\n", - "complex-p\n", - "(complex-p '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (complex-p '|YHBN-MONOMER| ))\n", - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.complex_p(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.complex_p(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "reactions-of-protein\n", - "(reactions-of-protein '|CPLX0-7660| nil t )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|CPLX0-7660| nil t ))\n", - "reactions-of-protein\n", - "(reactions-of-protein '|CPLX0-8247| nil t )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|CPLX0-8247| nil t ))\n", - "[[u'|RXN0-4301|'], [u'|TRANS-RXN-132|']]\n", - "reactions-of-protein\n", - "(reactions-of-protein '|OPPC-MONOMER| t nil )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|OPPC-MONOMER| t nil ))\n", - "reactions-of-protein\n", - "(reactions-of-protein '|YHBN-MONOMER| t nil )\n", - "(with-organism (:org-id '|ECOLI|) (reactions-of-protein '|YHBN-MONOMER| t nil ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "check-protein-components?\n", - "Optional If true, check all components of this protein for catalyzed reactions. \n", - "Defaults to true. \n", - "check-protein-containers?\n", - "Optional If true, check the containers and modified forms of the protein for \n", - "catalyzed reactions. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_containers = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_components = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "protein-in-compartment-p\n", - "(protein-in-compartment-p '|CPLX0-7660| 'CCO-CYTOSOL )\n", - "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|CPLX0-7660| 'CCO-CYTOSOL ))\n", - "protein-in-compartment-p\n", - "(protein-in-compartment-p '|CPLX0-8247| 'CCO-CYTOSOL )\n", - "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|CPLX0-8247| 'CCO-CYTOSOL ))\n", - "[False, False]\n", - "protein-in-compartment-p\n", - "(protein-in-compartment-p '|OPPC-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) )\n", - "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|OPPC-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) ))\n", - "protein-in-compartment-p\n", - "(protein-in-compartment-p '|YHBN-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) )\n", - "(with-organism (:org-id '|ECOLI|) (protein-in-compartment-p '|YHBN-MONOMER| '(CCO-CYTOSOL CCO-MEMBRANE) ))\n", - "[u'|CCI-CYTOSOL-GN|', False]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "compartments\n", - "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", - "See frame 'CCO. \n", - "default-ok?\n", - "Keyword, Optional If true, then we return true if the reaction has no associated \n", - "compartment information, or one of its associated locations is a super-class of \n", - "one of the members of the compartments argument. \n", - "pwy\n", - "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", - "rxn is limited to the given child of |Pathways|. \n", - "loose?\n", - "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", - "are treated as being the same compartment. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = 'CCO-CYTOSOL'))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = ['CCO-CYTOSOL', 'CCO-MEMBRANE']))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-transporters-across\n", - "(all-transporters-across :membranes :all)\n", - "(with-organism (:org-id '|ECOLI|) (all-transporters-across :membranes :all))\n", - "[u'|MTR-MONOMER|', u'|G7942-MONOMER|', u'|NANT-MONOMER|', u'|B1006-MONOMER|', u'|YDHE-MONOMER|', u'|YDEA-MONOMER|', u'|PITA-MONOMER|', u'|YEIM-MONOMER|', u'|BCR-MONOMER|', u'|YGFO-MONOMER|']\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "membranes\n", - "Keyword Either :all or a list of instances of the class. Defaults to :all \n", - "'CCO‑MEMBRANE. \n", - "method\n", - "Either :location or :reaction‑compartments. :location will check the 'locations \n", - "slot, while :reaction‑compartments will examine the compartments of reaction \n", - "substrates. Default value is :location. \n", - "\"\"\"\n", - "\n", - "lst = ecoli.all_transporters_across(membranes = 'all')\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "autocatalytic-reactions-of-enzyme\n", - "(autocatalytic-reactions-of-enzyme '|CPLX0-7660| )\n", - "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|CPLX0-7660| ))\n", - "autocatalytic-reactions-of-enzyme\n", - "(autocatalytic-reactions-of-enzyme '|CPLX0-8247| )\n", - "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|CPLX0-8247| ))\n", - "[[], []]\n", - "autocatalytic-reactions-of-enzyme\n", - "(autocatalytic-reactions-of-enzyme '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|OPPC-MONOMER| ))\n", - "autocatalytic-reactions-of-enzyme\n", - "(autocatalytic-reactions-of-enzyme '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (autocatalytic-reactions-of-enzyme '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/ptools API - Operations on Reactions.ipynb b/examples/ptools API - Operations on Reactions.ipynb deleted file mode 100644 index 9300ed3..0000000 --- a/examples/ptools API - Operations on Reactions.ipynb +++ /dev/null @@ -1,122770 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import os\n", - "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", - "\n", - "sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[u'|META|', u'|ECOLI|']\n" - ] - } - ], - "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-15348| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|LACTALDREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PFLDEACTIV-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|OHMETPYRKIN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7094| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7298| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1137| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|BADH-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DMKCYT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5061| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|FES-OX-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16000| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6505| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PEPCARBOX-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2601| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MENCYT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7003| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CARNDETRU-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14505| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ADPREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5118| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CHEBTAPD-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16650| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MALATE-DEH-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DEPHOSICITDEHASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|GDPREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXNMETA-12672| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MYRISTOYLACYLTRAN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|COBINPGUANYLYLTRANS-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PROTEIN-KINASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5183| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ADENYL-KIN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-10658| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-16910| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16910| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-12473| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-12473| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-2942| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2942| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-16381| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16381| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|YIAE2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|YIAE2-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17355| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17355| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|D-PPENTOMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|D-PPENTOMUT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-14570| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14570| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-19340| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-19340| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5216| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5216| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-5741| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-5741| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17393| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17393| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|METBALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|METBALT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-9533| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-9533| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PROLINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PROLINE--TRNA-LIGASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-9660| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-9660| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DEOXYADENPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DEOXYADENPHOSPHOR-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|SPONTPRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|SPONTPRO-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-1144| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-1144| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5292| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5292| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5098| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5098| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17701| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17701| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ALCOHOL-DEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ALCOHOL-DEHYDROG-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6435| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6435| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6547| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6547| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DIAMACTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DIAMACTRANS-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-3241| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-3241| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-745| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-745| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5387| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5387| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17783| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17783| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-14883| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14883| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|1.3.1.9-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|1.3.1.9-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|R170-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|R170-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|2.7.3.9-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|2.7.3.9-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DLACTDEHYDROGNAD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DLACTDEHYDROGNAD-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|N-ACETYLTRANSFER-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|N-ACETYLTRANSFER-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ARCB-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ARCB-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5435| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5435| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|CHEBTSRD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CHEBTSRD-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17799| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17799| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|TAGAKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TAGAKIN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ENOYL-ACP-REDUCT-NADPH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ENOYL-ACP-REDUCT-NADPH-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RIBOSYLHOMOCYSTEINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RIBOSYLHOMOCYSTEINASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|NARLX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|NARLX-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DUTP-PYROP-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DUTP-PYROP-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|AMINOBUTDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|AMINOBUTDEHYDROG-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|PYRUFLAVREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|PYRUFLAVREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-16330| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-16330| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6359| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6359| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-10661| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-10661| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5245| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5245| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17935| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17935| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-385| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-385| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-14107| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14107| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6490| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6490| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-10851| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-10851| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17014| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17014| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17661| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17661| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-10981| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-10981| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-15140| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-15140| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-17474| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-17474| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-5254| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-5254| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|FMNREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|FMNREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-19445| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-19445| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6954| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6954| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-6462| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-6462| ))\n", - "genes-of-reaction\n", - 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"genes-of-reaction\n", - "(genes-of-reaction '|RXN-14882| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14882| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|KDO-8PPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|KDO-8PPHOSPHAT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DMK-FE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DSBDC-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|TAGAALDOL-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7230| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|MEN-FE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|AMINEPHEN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7048| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-384| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7096| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-15139| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-5068| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-2022| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-7310| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|THREOSPON-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|CYTC-RED-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|ARGSUCCINSYN-RXN| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN-14394| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-3141| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|RXN0-4342| ))\n", - "genes-of-reaction\n", - "(genes-of-reaction '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-of-reaction '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|G6350|'],\n", - " [u'|EG10754|'],\n", - " [],\n", - " [],\n", - " [],\n", - " [u'|EG10068|'],\n", - " [u'|EG10278|', u'|G7213|'],\n", - " [],\n", - " [u'|G7590|'],\n", - " []]" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.genes_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-15348| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|LACTALDREDUCT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PFLDEACTIV-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|OHMETPYRKIN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7094| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7298| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1137| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|BADH-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DMKCYT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5061| ))\n", - 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"(substrates-of-reaction '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MENCYT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7003| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|CARNDETRU-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14505| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ADPREDUCT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-5118| )\n", - 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"(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|GDPREDUCT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXNMETA-12672| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MYRISTOYLACYLTRAN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|COBINPGUANYLYLTRANS-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PROTEIN-KINASE-RXN| ))\n", - "substrates-of-reaction\n", - 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"(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2942| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-16381| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-16381| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|YIAE2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|YIAE2-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-17355| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-17355| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|D-PPENTOMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|D-PPENTOMUT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-14570| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14570| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-19340| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-19340| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-5216| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-5216| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-5741| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-5741| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-17393| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-17393| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|METBALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|METBALT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-9533| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-9533| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|PROLINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|PROLINE--TRNA-LIGASE-RXN| ))\n", - "substrates-of-reaction\n", - 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"substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-14569| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14569| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|MERCAPYSTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MERCAPYSTRANS-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-1401| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-1401| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|SPERMIDINESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|SPERMIDINESYN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7049| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7049| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", - 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"(substrates-of-reaction '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DMK-FE-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DSBDC-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|TAGAALDOL-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7230| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|MEN-FE-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|AMINEPHEN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7048| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-384| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7096| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-15139| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-5068| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-2022| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-7310| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|THREOSPON-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|CYTC-RED-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|ARGSUCCINSYN-RXN| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN-14394| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-3141| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|RXN0-4342| ))\n", - "substrates-of-reaction\n", - "(substrates-of-reaction '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (substrates-of-reaction '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|NICOTINATE_NUCLEOTIDE|',\n", - " u'|ATP|',\n", - " u'|PROTON|',\n", - " u'|PPI|',\n", - " u'|DEAMIDO-NAD|'],\n", - " [u'|ACETALD|', u'|PYRUVATE|', u'|PROTON|', u'|ACETOIN|', u'|CARBON-DIOXIDE|'],\n", - " [u'|Protein-Red-Disulfides|',\n", - " u'|MONOMER0-4152|',\n", - " u'|MONOMER0-4438|',\n", - " u'|Protein-Ox-Disulfides|'],\n", - " [u'|PROTON|', u'|AMINO-OXOBUT|', u'|AMINO-ACETONE|', u'|CARBON-DIOXIDE|'],\n", - " [u'|Cytochromes-B-Reduced|', u'|Cytochromes-B|', u'|Reduced-Cytochromes-o|'],\n", - " [u'|ATP|',\n", - " u'|L-CITRULLINE|',\n", - " u'|L-ASPARTATE|',\n", - " u'|PROTON|',\n", - " u'|L-ARGININO-SUCCINATE|',\n", - " u'|PPI|',\n", - " u'|AMP|'],\n", - " [u'|ACETYL-COA|', u'|CPD-7221|', u'|CPD-15244|', u'|CO-A|'],\n", - " [u'|MONOMER0-1641|', u'|TORR-CPLX|', u'|CPLX0-2821|'],\n", - " [u'|ATP|',\n", - " u'|D-BETA-D-HEPTOSE-1-P|',\n", - " u'|PROTON|',\n", - " u'|ADP-D-GLYCERO-D-MANNO-HEPTOSE|',\n", - " u'|PPI|'],\n", - " [u'|DSBD-MONOMER|', u'|CPLX0-8004|', u'|DSBG-MONOMER|', u'|DSBDOXI-MONOMER|']]" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.substrates_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-15348| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15348| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|LACTALDREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|LACTALDREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|PFLDEACTIV-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PFLDEACTIV-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|OHMETPYRKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRIPHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRIPHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|EVGA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|EVGA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-17751| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-17751| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-11845| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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"(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14511| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-6385| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6385| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-1623| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-1623| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-6533| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6533| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|PGLUCISOM-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PGLUCISOM-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|MALIC-NADP-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|MALIC-NADP-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7105| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7105| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|UDPMANACATRANS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|UDPMANACATRANS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7303| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7303| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|CHD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CHD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|SAICARSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|SAICARSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN0-583| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-583| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-5125| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-5125| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|2.3.1.49-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|2.3.1.49-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-16687| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-16687| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|ADENYLYLSULFKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ADENYLYLSULFKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|PALMITOTRANS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PALMITOTRANS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-9983| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-9983| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RSTB-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RSTB-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14143| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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"(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|GUANYLCYC-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(enzymes-of-reaction '|TRANS-RXN0-595| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-595| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|FUCPALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|FUCPALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-8992| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-8992| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - 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"text": [ - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-1603| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN0-500| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-500| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-19776| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-19776| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14812| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14812| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7244| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|CYTIDEAM2-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CYTIDEAM2-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|AGMATIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|AGMATIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7124| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7124| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|3.2.2.21-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-17755| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-17755| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-1381| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-1381| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-16688| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-16688| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN-272| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|PGPPHOSPHA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|PGPPHOSPHA-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|COBINAMIDEKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|COBINAMIDEKIN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|ABC-12-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ABC-12-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-5182| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-271| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-271| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN0-491| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-491| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|3.1.26.12-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|3.1.26.12-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-5121| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN-165| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN-165| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-17916| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-17916| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|MALSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|MALSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-17652| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|THYMIDYLATE-5-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THYMIDYLATE-5-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN0-478| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-478| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|GLUCOSE-6-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|GLUCOSE-6-PHOSPHATASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|ATPASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-8999| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-8999| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DEOXYRIBODIPYRIMIDINE-PHOTOLYASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-6373| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-6373| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14074| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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"(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|2-METHYLCITRATE-SYNTHASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TRANS-RXN0-601| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TRANS-RXN0-601| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-313| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-313| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-17781| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-17781| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-19253| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|F16BDEPHOS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|F16BDEPHOS-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-19381| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-19381| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|SERINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|SERINE--TRNA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|FORMATEDEHYDROG-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - 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"enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14255| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14255| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-1130| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-1130| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-3221| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-3221| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|UBIQUINOL-OX-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|UBIQUINOL-OX-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14882| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14882| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|KDO-8PPHOSPHAT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|KDO-8PPHOSPHAT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|DMK-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DMK-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|DSBDC-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DSBDC-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|TAGAALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|TAGAALDOL-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7230| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7230| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|MEN-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|MEN-FE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|AMINEPHEN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|AMINEPHEN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7048| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7048| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-384| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-384| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|ACETATE--COA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ACETATE--COA-LIGASE-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7096| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7096| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-15139| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-15139| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-5068| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-5068| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|NICONUCADENYLYLTRAN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|NICONUCADENYLYLTRAN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-2022| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-2022| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-7310| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-7310| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|THREOSPON-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|THREOSPON-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|CYTC-RED-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|CYTC-RED-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|ARGSUCCINSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|ARGSUCCINSYN-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN-14394| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN-14394| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-3141| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-3141| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|RXN0-4342| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|RXN0-4342| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n", - "enzymes-of-reaction\n", - "(enzymes-of-reaction '|DSBD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil)\n", - "(with-organism (:org-id '|ECOLI|) (enzymes-of-reaction '|DSBD-RXN| :species '|ECOLI| :experimental-only? nil :local-only-p nil))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|NICONUCADENYLYLTRAN-MONOMER|'],\n", - " [u'|PYRUVOXID-CPLX|'],\n", - " [],\n", - " [],\n", - " [],\n", - " [u'|CPLX0-238|'],\n", - " [u'|G7213-MONOMER|', u'|FADA-CPLX|'],\n", - " [],\n", - " [u'|CPLX0-3661|'],\n", - " []]" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "species\n", - "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", - "MetaCyc, only proteins found in those organisms will be returned. This list can \n", - "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", - "the documentation for the 'species slot‑unit for more information. Default value \n", - "is nil. \n", - "experimental-only?\n", - "Keyword, Optional When true, only return enzymes that have a non-computational \n", - "evidence code associated with it. \n", - "local-only-p\n", - "Keyword, Optional When true, only return enzymes that catalyze the specific form \n", - "of the reaction, as opposed to enzymes that are known to catalyze a more general \n", - "form (i.e., class) of the reaction. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.enzymes_of_reaction(rxn = rxn, species = u'|ECOLI|', \n", - " experimental_only = False, local_only_p = False))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-15348| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|LACTALDREDUCT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PFLDEACTIV-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|OHMETPYRKIN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7094| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|TRIOSEPISOMERIZATION-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7298| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-1137| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|BADH-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DMKCYT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5061| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|FES-OX-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16000| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-6505| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PEPCARBOX-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2601| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MENCYT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7003| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CARNDETRU-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14505| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ADPREDUCT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5118| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CHEBTAPD-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-16650| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MALATE-DEH-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DEPHOSICITDEHASE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|GDPREDUCT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXNMETA-12672| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MYRISTOYLACYLTRAN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|COBINPGUANYLYLTRANS-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|PROTEIN-KINASE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-5183| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ADENYL-KIN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-10658| ))\n", - 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"reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-3221| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-3221| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|UBIQUINOL-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|UBIQUINOL-OX-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-14882| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14882| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|KDO-8PPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|KDO-8PPHOSPHAT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DMK-FE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DSBDC-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|TAGAALDOL-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7230| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|MEN-FE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|AMINEPHEN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7048| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-384| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ACETATE--COA-LIGASE-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7096| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-15139| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-5068| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|NICONUCADENYLYLTRAN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-2022| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-7310| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|THREOSPON-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|CYTC-RED-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|ARGSUCCINSYN-RXN| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN-14394| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-3141| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|RXN0-4342| ))\n", - "reaction-reactants-and-products\n", - "(reaction-reactants-and-products '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-reactants-and-products '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[[u'|PROTON|', u'|ATP|', u'|NICOTINATE_NUCLEOTIDE|'],\n", - " [u'|PPI|', u'|DEAMIDO-NAD|']],\n", - " [[u'|PROTON|', u'|PYRUVATE|', u'|ACETALD|'],\n", - " [u'|ACETOIN|', u'|CARBON-DIOXIDE|']],\n", - " [[u'|MONOMER0-4152|', u'|Protein-Red-Disulfides|'],\n", - " [u'|MONOMER0-4438|', u'|Protein-Ox-Disulfides|']],\n", - " [[u'|AMINO-OXOBUT|', u'|PROTON|'], [u'|AMINO-ACETONE|', u'|CARBON-DIOXIDE|']],\n", - " [[u'|Cytochromes-B-Reduced|', u'|Cytochromes-B|'],\n", - " [u'|Cytochromes-B|', u'|Reduced-Cytochromes-o|']],\n", - " [[u'|L-ASPARTATE|', u'|L-CITRULLINE|', u'|ATP|'],\n", - " [u'|PROTON|', u'|L-ARGININO-SUCCINATE|', u'|PPI|', u'|AMP|']],\n", - " [[u'|CPD-15244|', u'|CO-A|'], [u'|CPD-7221|', u'|ACETYL-COA|']],\n", - " None,\n", - " [[u'|PROTON|', u'|D-BETA-D-HEPTOSE-1-P|', u'|ATP|'],\n", - " [u'|ADP-D-GLYCERO-D-MANNO-HEPTOSE|', u'|PPI|']],\n", - " None]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "direction\n", - "Keyword, Optional Can take on the following values:\n", - "\n", - ":L2R\n", - "The reaction direction goes from ‘left to right’, as described in the \n", - "|Reactions| instance. \n", - ":R2L\n", - "The reaction direction goes from ‘right to left’; the opposite of what is \n", - "described in the |Reactions| instance. \n", - "\n", - "pwy\n", - "Keyword, Optional An instance of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.reaction_reactants_and_products(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "reaction-type\n", - "(reaction-type '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-15348| ))\n", - "reaction-type\n", - "(reaction-type '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|LACTALDREDUCT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PFLDEACTIV-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|OHMETPYRKIN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7094| ))\n", - "reaction-type\n", - "(reaction-type '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|TRIOSEPISOMERIZATION-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7298| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-1137| ))\n", - "reaction-type\n", - "(reaction-type '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|BADH-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DMKCYT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5061| ))\n", - "reaction-type\n", - "(reaction-type '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|FES-OX-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-16000| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-6505| ))\n", - "reaction-type\n", - "(reaction-type '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PEPCARBOX-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2601| ))\n", - "reaction-type\n", - "(reaction-type '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|MENCYT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7003| ))\n", - "reaction-type\n", - "(reaction-type '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|CARNDETRU-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14505| ))\n", - "reaction-type\n", - "(reaction-type '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ADPREDUCT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5118| ))\n", - "reaction-type\n", - "(reaction-type '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|CHEBTAPD-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-16650| ))\n", - "reaction-type\n", - "(reaction-type '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|MALATE-DEH-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DEPHOSICITDEHASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|GDPREDUCT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXNMETA-12672| ))\n", - "reaction-type\n", - "(reaction-type '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|MYRISTOYLACYLTRAN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|COBINPGUANYLYLTRANS-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PROTEIN-KINASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5183| ))\n", - "reaction-type\n", - "(reaction-type '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ADENYL-KIN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-10658| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-16910| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-16910| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-12473| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-12473| ))\n", - "reaction-type\n", - "(reaction-type '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-2942| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2942| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-16381| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-16381| ))\n", - "reaction-type\n", - "(reaction-type '|YIAE2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|YIAE2-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-17355| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-17355| ))\n", - "reaction-type\n", - "(reaction-type '|D-PPENTOMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|D-PPENTOMUT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14570| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14570| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-19340| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-19340| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5216| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5216| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-5741| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-5741| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-17393| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-17393| ))\n", - "reaction-type\n", - "(reaction-type '|METBALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|METBALT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-9533| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-9533| ))\n", - "reaction-type\n", - "(reaction-type '|PROLINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|PROLINE--TRNA-LIGASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-9660| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-9660| ))\n", - "reaction-type\n", - "(reaction-type '|DEOXYADENPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DEOXYADENPHOSPHOR-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|SPONTPRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|SPONTPRO-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-1144| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-1144| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5292| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5292| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-5098| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-5098| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-17701| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-17701| ))\n", - "reaction-type\n", - "(reaction-type '|ALCOHOL-DEHYDROG-RXN| )\n", - 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"reaction-type\n", - "(reaction-type '|ERYTH4PDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ERYTH4PDEHYDROG-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|ACNEULY-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ACNEULY-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14113| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14113| ))\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "reaction-type\n", - "(reaction-type '|RXN0-6389| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-6389| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-2584| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2584| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14503| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14503| ))\n", - "reaction-type\n", - "(reaction-type '|IGPSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|IGPSYN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|LYXK-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|LYXK-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXNMETA-12671| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXNMETA-12671| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7139| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7139| ))\n", - "reaction-type\n", - "(reaction-type '|ADENPRIBOSYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ADENPRIBOSYLTRAN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-2941| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2941| ))\n", - "reaction-type\n", - "(reaction-type '|5-NUCLEOTID-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|5-NUCLEOTID-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14569| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14569| ))\n", - "reaction-type\n", - "(reaction-type '|MERCAPYSTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|MERCAPYSTRANS-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-1401| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-1401| ))\n", - "reaction-type\n", - "(reaction-type '|SPERMIDINESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|SPERMIDINESYN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7049| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7049| ))\n", - "reaction-type\n", - "(reaction-type '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14255| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14255| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-1130| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-1130| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-3221| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-3221| ))\n", - "reaction-type\n", - "(reaction-type '|UBIQUINOL-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|UBIQUINOL-OX-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14882| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14882| ))\n", - "reaction-type\n", - "(reaction-type '|KDO-8PPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|KDO-8PPHOSPHAT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DMK-FE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DSBDC-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|TAGAALDOL-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7230| ))\n", - "reaction-type\n", - "(reaction-type '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|MEN-FE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|AMINEPHEN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7048| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-384| ))\n", - "reaction-type\n", - "(reaction-type '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ACETATE--COA-LIGASE-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7096| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-15139| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-5068| ))\n", - "reaction-type\n", - "(reaction-type '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|NICONUCADENYLYLTRAN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-2022| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-7310| ))\n", - "reaction-type\n", - "(reaction-type '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|THREOSPON-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|CYTC-RED-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|ARGSUCCINSYN-RXN| ))\n", - "reaction-type\n", - "(reaction-type '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN-14394| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-3141| ))\n", - "reaction-type\n", - "(reaction-type '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|RXN0-4342| ))\n", - "reaction-type\n", - "(reaction-type '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-type '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[u'|SMALL-MOLECULE|',\n", - " u'|SMALL-MOLECULE|',\n", - " u'|PROTEIN-REACTION|',\n", - " u'|SMALL-MOLECULE|',\n", - " u'|PROTEIN-REACTION|',\n", - " u'|SMALL-MOLECULE|',\n", - " u'|SMALL-MOLECULE|',\n", - " u'|PROTEIN-REACTION|',\n", - " u'|SMALL-MOLECULE|',\n", - " u'|PROTEIN-REACTION|']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.reaction_type(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "reaction-without-sequenced-enzyme-p\n", - "(reaction-without-sequenced-enzyme-p '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (reaction-without-sequenced-enzyme-p '|RXN-15348| ))\n" - ] - }, - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_without_sequenced_enzyme_p\u001b[0;34m(self, rxn)\u001b[0m\n\u001b[1;32m 1077\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1078\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1079\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1080\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1081\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 351\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 352\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 353\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 354\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 355\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." - ] - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "complete?\n", - "Optional If true, the predicate will return true when there is any associated \n", - "gene without a sequence. If nil, the predicate will return true when all \n", - "associated genes are without a sequence. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.rxn_without_sequenced_enzyme_p(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is REACTION-WITHOUT-SEQUENCED-ENZYME-P, \n", - "# which only argument is a rxn" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-15348| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|LACTALDREDUCT-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PFLDEACTIV-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|OHMETPYRKIN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7094| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|TRIOSEPISOMERIZATION-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7298| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-1137| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|BADH-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DMKCYT-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5061| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|FES-OX-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-16000| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-6505| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PEPCARBOX-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-2601| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|MENCYT-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7003| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|CARNDETRU-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-14505| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ADPREDUCT-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5118| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|CHEBTAPD-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-16650| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|MALATE-DEH-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DEPHOSICITDEHASE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|GDPREDUCT-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXNMETA-12672| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|MYRISTOYLACYLTRAN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|COBINPGUANYLYLTRANS-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|PROTEIN-KINASE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-5183| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ADENYL-KIN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-10658| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-16910| )\n", - 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"pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7230| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|MEN-FE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|AMINEPHEN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7048| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-384| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ACETATE--COA-LIGASE-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7096| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-15139| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-5068| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|NICONUCADENYLYLTRAN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-2022| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-7310| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|THREOSPON-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|CYTC-RED-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|ARGSUCCINSYN-RXN| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN-14394| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-3141| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|RXN0-4342| ))\n", - "pathway-hole-p\n", - "(pathway-hole-p '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (pathway-hole-p '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "hole-if-any-gene-without-position?\n", - "Keyword, Optional If true, then genes without specified coordinates for the \n", - "current organism’s genome are not counted when determining the status of the \n", - "reaction.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.pathway_hole_p(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxn-present?\n", - "(rxn-present? '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-present? '|RXN-15348| ))\n" - ] - }, - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1105\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1106\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1107\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1108\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1109\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 351\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 352\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 353\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 354\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 355\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." - ] - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.rxn_present_p(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is RXN-PRESENT?" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|RXN-15348| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN-15348| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|LACTALDREDUCT-RXN| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|LACTALDREDUCT-RXN| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|PFLDEACTIV-RXN| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|PFLDEACTIV-RXN| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|OHMETPYRKIN-RXN| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|OHMETPYRKIN-RXN| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|RXN0-7094| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7094| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|TRIOSEPISOMERIZATION-RXN| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|TRIOSEPISOMERIZATION-RXN| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|RXN0-7298| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-7298| '|RXN0-3741| ))\n", - 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"rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|RXN0-4342| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|RXN0-4342| '|RXN0-3741| ))\n", - "rxn-specific-form-of-rxn-p\n", - "(rxn-specific-form-of-rxn-p '|DSBD-RXN| '|RXN0-3741| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-specific-form-of-rxn-p '|DSBD-RXN| '|RXN0-3741| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "specific-rxn\n", - "A child of the class |Reactions|. \n", - "generic-rxn\n", - "A child of the class |Reactions|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.rxn_specific_form_of_rxn_p(specific_rxn = rxn, generic_rxn = u'|RXN0-3741|'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - 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] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.nonspecific_forms_of_rxn(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-15348| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|LACTALDREDUCT-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|PFLDEACTIV-RXN| ))\n", - "specific-forms-of-rxn\n", - 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"(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|MEN-FE-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|AMINEPHEN-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7048| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-384| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|ACETATE--COA-LIGASE-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7096| ))\n", - "specific-forms-of-rxn\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(specific-forms-of-rxn '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-15139| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-5068| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|NICONUCADENYLYLTRAN-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-2022| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-7310| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|THREOSPON-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|CYTC-RED-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|ARGSUCCINSYN-RXN| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN-14394| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-3141| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|RXN0-4342| ))\n", - "specific-forms-of-rxn\n", - "(specific-forms-of-rxn '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (specific-forms-of-rxn '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.specific_forms_of_rxn(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-15348| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-15348| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|LACTALDREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|LACTALDREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PFLDEACTIV-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PFLDEACTIV-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|OHMETPYRKIN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|OHMETPYRKIN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7094| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7094| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|TRIOSEPISOMERIZATION-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TRIOSEPISOMERIZATION-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7298| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7298| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-1137| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-1137| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|BADH-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|BADH-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|DMKCYT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DMKCYT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5061| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5061| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ACONITATE-DELTA-ISOMERASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ACONITATE-DELTA-ISOMERASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|FES-OX-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|FES-OX-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-16000| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16000| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-6505| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-6505| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PEPCARBOX-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PEPCARBOX-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-2601| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2601| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|MENCYT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MENCYT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|UDP-NACMURALGLDAPAALIG-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|UDP-NACMURALGLDAPAALIG-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7003| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7003| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|CARNDETRU-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CARNDETRU-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-14505| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14505| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ADPREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ADPREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5118| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5118| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|CHEBTAPD-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CHEBTAPD-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-16650| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16650| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|MALATE-DEH-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MALATE-DEH-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|DEPHOSICITDEHASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DEPHOSICITDEHASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PHENPRODIOLDEHYDROG-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHENPRODIOLDEHYDROG-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|GDPREDUCT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|GDPREDUCT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|URIDINE-NUCLEOSIDASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|URIDINE-NUCLEOSIDASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXNMETA-12672| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXNMETA-12672| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|MYRISTOYLACYLTRAN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MYRISTOYLACYLTRAN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|COBINPGUANYLYLTRANS-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|COBINPGUANYLYLTRANS-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PROTEIN-KINASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PROTEIN-KINASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5183| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5183| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ADENYL-KIN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ADENYL-KIN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-10658| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-10658| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-16910| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16910| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-12473| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-12473| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-2942| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2942| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-16381| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-16381| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|YIAE2-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|YIAE2-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-17355| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17355| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|D-PPENTOMUT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|D-PPENTOMUT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-14570| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14570| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-19340| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-19340| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5216| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5216| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-5741| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-5741| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-17393| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17393| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|METBALT-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|METBALT-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-9533| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-9533| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PROLINE--TRNA-LIGASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PROLINE--TRNA-LIGASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-9660| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-9660| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|DEOXYADENPHOSPHOR-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DEOXYADENPHOSPHOR-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|SPONTPRO-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|SPONTPRO-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-1144| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-1144| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5292| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5292| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-5098| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-5098| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-17701| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-17701| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ALCOHOL-DEHYDROG-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ALCOHOL-DEHYDROG-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-6435| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-6435| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PYRIDOXINE-4-DEHYDROGENASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PYRIDOXINE-4-DEHYDROGENASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-6547| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-6547| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|DIAMACTRANS-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DIAMACTRANS-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-3241| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-3241| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-745| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-745| '(|CCO_CYTOSOL|) ))\n", - 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] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|PHOBR-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|PHOBR-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-293| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-293| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-14510| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14510| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-10654| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-10654| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-4741| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-4741| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - 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"(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|TAGAALDOL-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7230| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7230| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|MEN-FE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|MEN-FE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|AMINEPHEN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|AMINEPHEN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7048| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7048| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-384| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-384| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ACETATE--COA-LIGASE-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ACETATE--COA-LIGASE-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7096| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7096| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-15139| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-15139| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-5068| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-5068| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|NICONUCADENYLYLTRAN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|NICONUCADENYLYLTRAN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-2022| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-2022| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-7310| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-7310| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|THREOSPON-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|THREOSPON-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|CYTC-RED-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|CYTC-RED-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|ARGSUCCINSYN-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|ARGSUCCINSYN-RXN| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN-14394| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN-14394| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-3141| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-3141| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|RXN0-4342| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|RXN0-4342| '(|CCO_CYTOSOL|) ))\n", - "rxn-in-compartment-p\n", - "(rxn-in-compartment-p '|DSBD-RXN| '(|CCO_CYTOSOL|) )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-in-compartment-p '|DSBD-RXN| '(|CCO_CYTOSOL|) ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "compartments\n", - "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", - "See frame 'CCO. \n", - "default-ok?\n", - "Keyword, Optional If true, then we return true if the reaction has no associated \n", - "compartment information, or one of its associated locations is a super-class of \n", - "one of the members of the compartments argument. \n", - "pwy\n", - "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", - "rxn is limited to the given child of |Pathways|. \n", - "loose?\n", - "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", - "are treated as being the same compartment.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.rxn_in_compartment_p(rxn = rxn, compartments = [u'|CCO_CYTOSOL|']))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "compartment-of-rxn\n", - "(compartment-of-rxn '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (compartment-of-rxn '|RXN-15348| ))\n" - ] - }, - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1204\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCCO\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1205\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1206\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1207\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1208\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 376\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 378\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 379\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 380\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mis_a_class_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclassName\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 344\u001b[0m \u001b[0mlisp_query\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'(with-organism (:org-id \\''\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_orgid\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m') '\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 345\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0mlisp_query\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 181\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mbasestring\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 182\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 183\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" - ] - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "default\n", - "Optional The default compartment for reactions without any compartment \n", - "annotations on their substrates. The default value is 'CCO‑CYTOSOL. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.compartment_of_rxn(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is missing (?)" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-15348| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|LACTALDREDUCT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PFLDEACTIV-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|OHMETPYRKIN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7094| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|TRIOSEPISOMERIZATION-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|TRIOSEPISOMERIZATION-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7298| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7298| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-1137| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1137| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|BADH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|BADH-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DMKCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DMKCYT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5061| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5061| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACONITATE-DELTA-ISOMERASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|FES-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|FES-OX-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-16000| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16000| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-6505| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-6505| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PEPCARBOX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PEPCARBOX-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-2601| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2601| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|MENCYT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MENCYT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|UDP-NACMURALGLDAPAALIG-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7003| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7003| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|CARNDETRU-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CARNDETRU-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-14505| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14505| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ADPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ADPREDUCT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5118| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5118| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|CHEBTAPD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CHEBTAPD-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-16650| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16650| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|MALATE-DEH-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MALATE-DEH-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DEPHOSICITDEHASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DEPHOSICITDEHASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PHENPRODIOLDEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PHENPRODIOLDEHYDROG-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|GDPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|GDPREDUCT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|URIDINE-NUCLEOSIDASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXNMETA-12672| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXNMETA-12672| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|MYRISTOYLACYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MYRISTOYLACYLTRAN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|COBINPGUANYLYLTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|COBINPGUANYLYLTRANS-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PROTEIN-KINASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PROTEIN-KINASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5183| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5183| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ADENYL-KIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ADENYL-KIN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-10658| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-10658| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-16910| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16910| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-12473| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-12473| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PHOSPHOGLYCERATE-PHOSPHATASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-2942| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2942| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-16381| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-16381| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|YIAE2-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|YIAE2-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-17355| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17355| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|D-PPENTOMUT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|D-PPENTOMUT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-14570| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14570| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-19340| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-19340| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5216| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5216| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-5741| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-5741| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-17393| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17393| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|METBALT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|METBALT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-9533| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-9533| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PROLINE--TRNA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PROLINE--TRNA-LIGASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-9660| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-9660| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DEOXYADENPHOSPHOR-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DEOXYADENPHOSPHOR-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|SPONTPRO-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|SPONTPRO-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-1144| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1144| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5292| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5292| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5098| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5098| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-17701| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-17701| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ALCOHOL-DEHYDROG-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ALCOHOL-DEHYDROG-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-6435| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-6435| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|PYRIDOXINE-4-DEHYDROGENASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-6547| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-6547| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DIAMACTRANS-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DIAMACTRANS-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-3241| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-3241| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-745| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-745| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-5387| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-5387| ))\n", - 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"compartments-of-reaction\n", - "(compartments-of-reaction '|SPERMIDINESYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|SPERMIDINESYN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7049| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7049| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ALCOHOL-DEHYDROG-GENERIC-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-14255| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14255| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-1130| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-1130| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-3221| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-3221| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|UBIQUINOL-OX-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|UBIQUINOL-OX-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-14882| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14882| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|KDO-8PPHOSPHAT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|KDO-8PPHOSPHAT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DMK-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DMK-FE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|N-ACETYLGLUTPREDUCT-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DSBDC-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DSBDC-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|TAGAALDOL-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|TAGAALDOL-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7230| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7230| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|MEN-FE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|MEN-FE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|AMINEPHEN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|AMINEPHEN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7048| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7048| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-384| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-384| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ACETATE--COA-LIGASE-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ACETATE--COA-LIGASE-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7096| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7096| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-15139| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-15139| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-5068| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-5068| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|NICONUCADENYLYLTRAN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|NICONUCADENYLYLTRAN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-2022| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-2022| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-7310| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-7310| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|THREOSPON-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|THREOSPON-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|CYTC-RED-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|CYTC-RED-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|ARGSUCCINSYN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|ARGSUCCINSYN-RXN| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN-14394| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN-14394| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-3141| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-3141| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|RXN0-4342| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|RXN0-4342| ))\n", - "compartments-of-reaction\n", - "(compartments-of-reaction '|DSBD-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (compartments-of-reaction '|DSBD-RXN| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-PERI-BAC|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-CYTOSOL|'],\n", - " [u'|CCO-PERI-BAC|']]" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "sides\n", - "Keyword, Optional The slots of the reaction to consider. The default value is \n", - "'(LEFT RIGHT). \n", - "default-compartment\n", - "The default compartment, as determined by the function (default‑compartment), \n", - "which currently is set to 'CCO‑CYTOSOL.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.compartments_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::transport )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::transport ))\n", - "transported-chemicals\n", - "(transported-chemicals '|TRANS-RXN-145| )\n", - "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-145| ))\n", - "transported-chemicals\n", - "(transported-chemicals '|RXN0-7221| )\n", - "(with-organism (:org-id '|ECOLI|) (transported-chemicals '|RXN0-7221| ))\n", - "transported-chemicals\n", - "(transported-chemicals '|TRANS-RXN0-212| )\n", - 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"(with-organism (:org-id '|ECOLI|) (transported-chemicals '|TRANS-RXN-1| ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[u'|Nucleosides|'],\n", - " [u'|D-ALANINE|', u'|PROTON|'],\n", - " [u'|GUANINE|'],\n", - " [u'|DEOXYINOSINE|', u'|PROTON|'],\n", - " [u'|PROTON|', u'|CPD0-2241|'],\n", - " [u'|Inorganic-Compounds|'],\n", - " [u'|PROTON|', u'|D-GALACTURONATE|'],\n", - " [u'|CPD0-2486|'],\n", - " [u'|MELIBIOSE|', u'|LI+|'],\n", - " [u'|FORMATE|']]" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "side\n", - "Keyword, Optional The side of the reaction from which to return the transported \n", - "compound. \n", - "primary-only?\n", - "Keyword, Optional If true, then filter out common exchangers (currently defined \n", - "as '(PROTON NA CPD-1)+). If true, and the only transported compounds are in this \n", - "list, then the filter doesn’t apply. \n", - "from-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", - "return compounds transported from that compartment. \n", - "to-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", - "return compounds transported to that compartment. \n", - "show-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, and the \n", - "compound is modified during transport, then only return the form of the compound \n", - "as found in this compartment. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':transport'):\n", - " lst.append(ecoli.transported_chemicals(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "get-predecessors\n", - "(get-predecessors '|RXN-15348| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-15348| 'PWY0-1347 ))\n", - "get-predecessors\n", - "(get-predecessors '|LACTALDREDUCT-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|LACTALDREDUCT-RXN| 'PWY0-1347 ))\n", - "get-predecessors\n", - "(get-predecessors '|PFLDEACTIV-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|PFLDEACTIV-RXN| 'PWY0-1347 ))\n", - 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"(get-predecessors '|RXN-14394| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN-14394| 'PWY0-1347 ))\n", - "get-predecessors\n", - "(get-predecessors '|RXN0-3141| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-3141| 'PWY0-1347 ))\n", - "get-predecessors\n", - "(get-predecessors '|RXN0-4342| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|RXN0-4342| 'PWY0-1347 ))\n", - "get-predecessors\n", - "(get-predecessors '|DSBD-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-predecessors '|DSBD-RXN| 'PWY0-1347 ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "A child of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.get_predecessors(rxn = rxn, pwy = u'PWY0-1347'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "get-successors\n", - "(get-successors '|RXN-15348| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-15348| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|LACTALDREDUCT-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|LACTALDREDUCT-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|PFLDEACTIV-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|PFLDEACTIV-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|OHMETPYRKIN-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|OHMETPYRKIN-RXN| 'PWY0-1347 ))\n", - 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"(with-organism (:org-id '|ECOLI|) (get-successors '|NICONUCADENYLYLTRAN-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|RXN0-2022| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-2022| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|RXN0-7310| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-7310| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|THREOSPON-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|THREOSPON-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|CYTC-RED-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|CYTC-RED-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|ARGSUCCINSYN-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|ARGSUCCINSYN-RXN| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|RXN-14394| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN-14394| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|RXN0-3141| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-3141| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|RXN0-4342| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|RXN0-4342| 'PWY0-1347 ))\n", - "get-successors\n", - "(get-successors '|DSBD-RXN| 'PWY0-1347 )\n", - "(with-organism (:org-id '|ECOLI|) (get-successors '|DSBD-RXN| 'PWY0-1347 ))\n" - ] - }, - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "A child of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.get_successors(rxn = rxn, pwy = u'PWY0-1347'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "all-rxns\n", - "(all-rxns ::all )\n", - "(with-organism (:org-id '|ECOLI|) (all-rxns ::all ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|RXN-15348| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN-15348| ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|LACTALDREDUCT-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|LACTALDREDUCT-RXN| ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|PFLDEACTIV-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|PFLDEACTIV-RXN| ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|OHMETPYRKIN-RXN| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|OHMETPYRKIN-RXN| ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|RXN0-7094| )\n", - "(with-organism (:org-id '|ECOLI|) (rxn-w-isozymes-p '|RXN0-7094| ))\n", - "rxn-w-isozymes-p\n", - "(rxn-w-isozymes-p '|TRIOSEPISOMERIZATION-RXN| )\n", - 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}, - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, True, False, False, False]" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type = ':all'):\n", - " lst.append(ecoli.rxn_w_isozymes_p(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/ptools API - Operations on Regulation Frames.ipynb b/examples/ptools API - Operations on Regulation Frames.ipynb deleted file mode 100644 index 9a089b8..0000000 --- a/examples/ptools API - Operations on Regulation Frames.ipynb +++ /dev/null @@ -1,1411 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/glucksfall/Dropbox/modding-pythoncyc/PythonCyc']" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import os\n", - "import sys\n", - "module_path = os.path.abspath(os.path.join('./PythonCyc/'))\n", - "sys.path = [module_path]\n", - "\n", - "sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rm: cannot remove './PythonCyc/pythoncyc/*pyc': No such file or directory\n", - "[u'|META|', u'|ECOLI|']\n", - "class-name-p\n", - "(class-name-p \"regulation\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"regulation\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Regulation| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Regulation| ))\n", - "get-class\n", - "(get-class |Regulation| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Regulation| ))\n", - "class-name-p\n", - "(class-name-p \"genes\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"genes\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Genes| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Genes| ))\n", - "get-class\n", - "(get-class |Genes| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Genes| ))\n", - "class-name-p\n", - "(class-name-p \"proteins\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"proteins\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Proteins| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Proteins| ))\n", - "get-class\n", - "(get-class |Proteins| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Proteins| ))\n", - "class-name-p\n", - "(class-name-p \"transcription_units\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"transcription_units\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Transcription-Units| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Transcription-Units| ))\n", - "get-class\n", - "(get-class |Transcription-Units| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Transcription-Units| ))\n", - "class-name-p\n", - "(class-name-p \"DNA_Binding_Sites\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"DNA_Binding_Sites\" ))\n", - "get-frame-object\n", - "(get-frame-object '|DNA-Binding-Sites| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|DNA-Binding-Sites| ))\n", - "get-class\n", - "(get-class |DNA-Binding-Sites| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |DNA-Binding-Sites| ))\n", - "class-name-p\n", - "(class-name-p \"mRNA_Binding_Sites\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"mRNA_Binding_Sites\" ))\n", - "get-frame-object\n", - "(get-frame-object '|mRNA-Binding-Sites| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|mRNA-Binding-Sites| ))\n", - "get-class\n", - "(get-class |mRNA-Binding-Sites| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |mRNA-Binding-Sites| ))\n", - "class-name-p\n", - "(class-name-p \"Terminators\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"Terminators\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Terminators| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Terminators| ))\n", - "get-class\n", - "(get-class |Terminators| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Terminators| ))\n", - "class-name-p\n", - "(class-name-p \"Promoters\" )\n", - "(with-organism (:org-id '|ECOLI|) (class-name-p \"Promoters\" ))\n", - "get-frame-object\n", - "(get-frame-object '|Promoters| )\n", - "(with-organism (:org-id '|ECOLI|) (get-frame-object '|Promoters| ))\n", - "get-class\n", - "(get-class |Promoters| )\n", - "(with-organism (:org-id '|ECOLI|) (get-class |Promoters| ))\n" - ] - } - ], - "source": [ - "# remove pyc files\n", - "!rm ./PythonCyc/pythoncyc/*pyc\n", - "\n", - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print all_orgids\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "\n", - "regs = [x.frameid for x in ecoli.regulation.instances][0:2]\n", - "genes = [x.frameid for x in ecoli.genes.instances][0:2]\n", - "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", - "tus = [x.frameid for x in ecoli.transcription_units.instances][0:2]\n", - "dna_sites = [x.frameid for x in ecoli.DNA_Binding_Sites.instances][0:2]\n", - "mrna_sites = [x.frameid for x in ecoli.mRNA_Binding_Sites.instances][0:2]\n", - "terminators = [x.frameid for x in ecoli.Terminators.instances][0:2]\n", - "promoters = [x.frameid for x in ecoli.Promoters.instances][0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "activation-p\n", - "(activation-p '|REG0-5116| )\n", - "(with-organism (:org-id '|ECOLI|) (activation-p '|REG0-5116| ))\n", - "activation-p\n", - "(activation-p '|REG0-5024| )\n", - "(with-organism (:org-id '|ECOLI|) (activation-p '|REG0-5024| ))\n", - "[True, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.activation_p(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "inhibition-p\n", - "(inhibition-p '|REG0-5116| )\n", - "(with-organism (:org-id '|ECOLI|) (inhibition-p '|REG0-5116| ))\n", - "inhibition-p\n", - "(inhibition-p '|REG0-5024| )\n", - "(with-organism (:org-id '|ECOLI|) (inhibition-p '|REG0-5024| ))\n", - "[False, True]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.inhibition_p(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "direct-regulators\n", - "(direct-regulators '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-regulators '|EG11414| ))\n", - "direct-regulators\n", - "(direct-regulators '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-regulators '|EG11127| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_regulators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "direct-activators\n", - "(direct-activators '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-activators '|EG11414| ))\n", - "direct-activators\n", - "(direct-activators '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-activators '|EG11127| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_activators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "direct-inhibitors\n", - "(direct-inhibitors '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-inhibitors '|EG11414| ))\n", - "direct-inhibitors\n", - "(direct-inhibitors '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (direct-inhibitors '|EG11127| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_inhibitors(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-factor?\n", - "(transcription-factor? '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-factor? '|OPPC-MONOMER| ))\n" - ] - } - ], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_p(protein))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulator-of-type?\n", - "(regulator-of-type? '|OPPC-MONOMER| :activator )\n", - "(with-organism (:org-id '|ECOLI|) (regulator-of-type? '|OPPC-MONOMER| :activator ))\n" - ] - } - ], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.regulator_of_type(protein, class_name = ':activator'))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulon-of-protein\n", - "(regulon-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (regulon-of-protein '|OPPC-MONOMER| ))\n", - "regulon-of-protein\n", - "(regulon-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (regulon-of-protein '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.regulon_of_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulation-frame-transcription-units\n", - "(regulation-frame-transcription-units '|REG0-5116| )\n", - "(with-organism (:org-id '|ECOLI|) (regulation-frame-transcription-units '|REG0-5116| ))\n", - "regulation-frame-transcription-units\n", - "(regulation-frame-transcription-units '|REG0-5024| )\n", - "(with-organism (:org-id '|ECOLI|) (regulation-frame-transcription-units '|REG0-5024| ))\n", - "[[u'|TU162|'], [u'|TU461|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.regulation_frame_transcription_units(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-regulation-frames\n", - "(transcription-unit-regulation-frames '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-regulation-frames '|TU0-8814| ))\n", - "transcription-unit-regulation-frames\n", - "(transcription-unit-regulation-frames '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-regulation-frames '|TU0-8340| ))\n", - "[[], [u'|REG0-11053|', u'|REG0-11052|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_regulation_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-activation-frames\n", - "(transcription-unit-activation-frames '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-activation-frames '|TU0-8814| ))\n", - "transcription-unit-activation-frames\n", - "(transcription-unit-activation-frames '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-activation-frames '|TU0-8340| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_activation_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-inhibition-frames\n", - "(transcription-unit-inhibition-frames '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibition-frames '|TU0-8814| ))\n", - "transcription-unit-inhibition-frames\n", - "(transcription-unit-inhibition-frames '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibition-frames '|TU0-8340| ))\n", - "[[], [u'|REG0-11053|', u'|REG0-11052|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_inhibition_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-units-of-protein\n", - "(transcription-units-of-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-units-of-protein '|OPPC-MONOMER| ))\n", - "transcription-units-of-protein\n", - "(transcription-units-of-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-units-of-protein '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.transcription_units_of_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-regulated-by-protein\n", - "(genes-regulated-by-protein '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-protein '|OPPC-MONOMER| ))\n", - "genes-regulated-by-protein\n", - "(genes-regulated-by-protein '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-protein '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_regulated_by_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "DNA-binding-sites-of-protein\n", - "(DNA-binding-sites-of-protein '|OPPC-MONOMER| :all-forms? t)\n", - "(with-organism (:org-id '|ECOLI|) (DNA-binding-sites-of-protein '|OPPC-MONOMER| :all-forms? t))\n", - "DNA-binding-sites-of-protein\n", - "(DNA-binding-sites-of-protein '|YHBN-MONOMER| :all-forms? t)\n", - "(with-organism (:org-id '|ECOLI|) (DNA-binding-sites-of-protein '|YHBN-MONOMER| :all-forms? t))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.DNA_binding_sites_of_protein(protein, all_forms = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulator-proteins-of-transcription-unit\n", - "(regulator-proteins-of-transcription-unit '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (regulator-proteins-of-transcription-unit '|TU0-8814| ))\n", - "regulator-proteins-of-transcription-unit\n", - "(regulator-proteins-of-transcription-unit '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (regulator-proteins-of-transcription-unit '|TU0-8340| ))\n", - "[[], [u'|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.regulator_proteins_of_transcription_unit(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-factor-ligands\n", - "(transcription-factor-ligands '|OPPC-MONOMER| ::both )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-factor-ligands '|OPPC-MONOMER| ::both ))\n" - ] - } - ], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_ligands(protein, u':both'))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-factor-active-forms\n", - "(transcription-factor-active-forms '|OPPC-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-factor-active-forms '|OPPC-MONOMER| ))\n", - "transcription-factor-active-forms\n", - "(transcription-factor-active-forms '|YHBN-MONOMER| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-factor-active-forms '|YHBN-MONOMER| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_active_forms(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-regulating-gene\n", - "(genes-regulating-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulating-gene '|EG11414| ))\n", - "genes-regulating-gene\n", - "(genes-regulating-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulating-gene '|EG11127| ))\n", - "[[], [u'|G6761|', u'|EG10457|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.genes_regulating_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "genes-regulated-by-gene\n", - "(genes-regulated-by-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-gene '|EG11414| ))\n", - "genes-regulated-by-gene\n", - "(genes-regulated-by-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (genes-regulated-by-gene '|EG11127| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.genes_regulated_by_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulators-of-gene\n", - "(regulators-of-gene '|EG11414| :by-function? t)\n", - "(with-organism (:org-id '|ECOLI|) (regulators-of-gene '|EG11414| :by-function? t))\n", - "regulators-of-gene\n", - "(regulators-of-gene '|EG11127| :by-function? t)\n", - "(with-organism (:org-id '|ECOLI|) (regulators-of-gene '|EG11127| :by-function? t))\n", - "[[None, None, None], [[u'|G6761-MONOMER|'], [u'|PD00288|'], None]]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.regulators_of_gene_transcription(gene, by_function = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-activators\n", - "(transcription-unit-activators '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-activators '|TU0-8814| ))\n", - "transcription-unit-activators\n", - "(transcription-unit-activators '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-activators '|TU0-8340| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_activators(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-inhibitors\n", - "(transcription-unit-inhibitors '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibitors '|TU0-8814| ))\n", - "transcription-unit-inhibitors\n", - "(transcription-unit-inhibitors '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-inhibitors '|TU0-8340| ))\n", - "[[], [u'|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_inhibitors(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "regulators-of-operon-transcription\n", - "(regulators-of-operon-transcription '(|TU0-8814|) t )\n", - "(with-organism (:org-id '|ECOLI|) (regulators-of-operon-transcription '(|TU0-8814|) t ))\n", - "regulators-of-operon-transcription\n", - "(regulators-of-operon-transcription '(|TU0-8340|) t )\n", - "(with-organism (:org-id '|ECOLI|) (regulators-of-operon-transcription '(|TU0-8340|) t ))\n", - "[[None, None, None], [None, [u'|PD01379|'], None]]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.regulators_of_operon_transcription(tu, by_function = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-promoter\n", - "(transcription-unit-promoter '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-promoter '|TU0-8814| ))\n", - "transcription-unit-promoter\n", - "(transcription-unit-promoter '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-promoter '|TU0-8340| ))\n", - "[None, u'|PM0-8720|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_promoter(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-genes\n", - "(transcription-unit-genes '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-genes '|TU0-8814| ))\n", - "transcription-unit-genes\n", - "(transcription-unit-genes '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-genes '|TU0-8340| ))\n", - "[[u'|G6954|'], [u'|EG11346|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_genes(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-first-gene\n", - "(transcription-unit-first-gene '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-first-gene '|TU0-8814| ))\n", - "transcription-unit-first-gene\n", - "(transcription-unit-first-gene '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-first-gene '|TU0-8340| ))\n", - "[u'|G6954|', u'|EG11346|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_first_gene(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-binding-sites\n", - "(transcription-unit-binding-sites '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-binding-sites '|TU0-8814| ))\n", - "transcription-unit-binding-sites\n", - "(transcription-unit-binding-sites '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-binding-sites '|TU0-8340| ))\n", - "[[], [u'|BS0-8048|', u'|BS0-8047|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_binding_sites(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-transcription-factors\n", - "(transcription-unit-transcription-factors '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-transcription-factors '|TU0-8814| ))\n", - "transcription-unit-transcription-factors\n", - "(transcription-unit-transcription-factors '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-transcription-factors '|TU0-8340| ))\n", - "[[], [u'|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_transcription_factors(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 33, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-mrna-binding-sites\n", - "(transcription-unit-mrna-binding-sites '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-mrna-binding-sites '|TU0-8814| ))\n", - "transcription-unit-mrna-binding-sites\n", - "(transcription-unit-mrna-binding-sites '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-mrna-binding-sites '|TU0-8340| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_mrna_binding_sites(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 34, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "chromosome-of-operon\n", - "(chromosome-of-operon '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-operon '|TU0-8814| ))\n", - "chromosome-of-operon\n", - "(chromosome-of-operon '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (chromosome-of-operon '|TU0-8340| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.chromosome_of_operon(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "binding-sites-affecting-gene\n", - "(binding-sites-affecting-gene '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-sites-affecting-gene '|EG11414| ))\n", - "binding-sites-affecting-gene\n", - "(binding-sites-affecting-gene '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-sites-affecting-gene '|EG11127| ))\n", - "[[], [u'|BS0-7937|', u'|BS0-7936|', u'|BS0-7935|', u'|BS0-7225|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.binding_sites_affecting_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "binding-site->regulators\n", - "(binding-site->regulators '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|EG11414| ))\n", - "binding-site->regulators\n", - "(binding-site->regulators '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|EG11127| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.binding_site_to_regulators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "binding-site->regulators\n", - "(binding-site->regulators '|BS0-1683| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|BS0-1683| ))\n", - "binding-site->regulators\n", - "(binding-site->regulators '|BS0-8256| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site->regulators '|BS0-8256| ))\n", - "[[u'|PHOSPHO-PHOB|'], [u'|CPLX0-7639|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_to_regulators(dna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 38, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-units-of-promoter\n", - "(transcription-units-of-promoter '|PM0-10506| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-units-of-promoter '|PM0-10506| ))\n", - "transcription-units-of-promoter\n", - "(transcription-units-of-promoter '|PM0-10035| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-units-of-promoter '|PM0-10035| ))\n", - "[[u'|TU0-13975|'], [u'|TU0-8636|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for promoter in promoters:\n", - " lst.append(ecoli.transcription_units_of_promoter(promoter))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "promoter-binding-sites\n", - "(promoter-binding-sites '|PM0-10506| )\n", - "(with-organism (:org-id '|ECOLI|) (promoter-binding-sites '|PM0-10506| ))\n", - "promoter-binding-sites\n", - "(promoter-binding-sites '|PM0-10035| )\n", - "(with-organism (:org-id '|ECOLI|) (promoter-binding-sites '|PM0-10035| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for promoter in promoters:\n", - " lst.append(ecoli.promoter_binding_sites(promoter))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-terminators\n", - "(transcription-unit-terminators '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-terminators '|TU0-8814| ))\n", - "transcription-unit-terminators\n", - "(transcription-unit-terminators '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-terminators '|TU0-8340| ))\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_terminators(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 41, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "containing-tus\n", - "(containing-tus '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|TU0-8814| ))\n", - "containing-tus\n", - "(containing-tus '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|TU0-8340| ))\n", - "[[u'|TU0-8814|'], [u'|TU0-8340|']]\n", - "containing-tus\n", - "(containing-tus '|RBS0-212| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|RBS0-212| ))\n", - "containing-tus\n", - "(containing-tus '|RBS0-96| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|RBS0-96| ))\n", - "[[u'|TU0-42642|', u'|TU0-42640|', u'|TU0-42638|', u'|TU0-42636|', u'|TU281|', u'|TU00342|'], [u'|TU00392|']]\n", - "containing-tus\n", - "(containing-tus '|BS0-1683| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|BS0-1683| ))\n", - "containing-tus\n", - "(containing-tus '|BS0-8256| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|BS0-8256| ))\n", - "[[u'|TU0-2021|'], [u'|TU0-13514|']]\n", - "containing-tus\n", - "(containing-tus '|PM0-10506| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|PM0-10506| ))\n", - "containing-tus\n", - "(containing-tus '|PM0-10035| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|PM0-10035| ))\n", - "[[u'|TU0-13975|'], [u'|TU0-8636|']]\n", - "containing-tus\n", - "(containing-tus '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|EG11414| ))\n", - "containing-tus\n", - "(containing-tus '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|EG11127| ))\n", - "[[u'|TU0-14216|'], [u'|TU0-36408|', u'|TU0-13193|']]\n", - "containing-tus\n", - "(containing-tus '|TERM1| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|TERM1| ))\n", - "containing-tus\n", - "(containing-tus '|TERM0881| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-tus '|TERM0881| ))\n", - "[[u'|TU-8390|', u'|TU-8389|'], [u'|TU00091|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in mrna_sites:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in dna_sites:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in promoters:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in genes:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in terminators:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "containing-chromosome\n", - "(containing-chromosome '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TU0-8814| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TU0-8340| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n", - "containing-chromosome\n", - "(containing-chromosome '|RBS0-212| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|RBS0-212| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|RBS0-96| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|RBS0-96| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n", - "containing-chromosome\n", - "(containing-chromosome '|BS0-1683| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|BS0-1683| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|BS0-8256| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|BS0-8256| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n", - "containing-chromosome\n", - "(containing-chromosome '|PM0-10506| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|PM0-10506| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|PM0-10035| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|PM0-10035| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n", - "containing-chromosome\n", - "(containing-chromosome '|EG11414| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|EG11414| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|EG11127| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|EG11127| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n", - "containing-chromosome\n", - "(containing-chromosome '|TERM1| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TERM1| ))\n", - "containing-chromosome\n", - "(containing-chromosome '|TERM0881| )\n", - "(with-organism (:org-id '|ECOLI|) (containing-chromosome '|TERM0881| ))\n", - "[u'|COLI-K12|', u'|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in mrna_sites:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in dna_sites:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in promoters:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in genes:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in terminators:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "binding-site-promoters\n", - "(binding-site-promoters '|BS0-1683| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-promoters '|BS0-1683| ))\n", - "binding-site-promoters\n", - "(binding-site-promoters '|BS0-8256| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-promoters '|BS0-8256| ))\n", - "[[u'|PM0-2201|'], [u'|PM0-9620|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_promoters(dna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "transcription-unit-all-components\n", - "(transcription-unit-all-components '|TU0-8814| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-all-components '|TU0-8814| ))\n", - "transcription-unit-all-components\n", - "(transcription-unit-all-components '|TU0-8340| )\n", - "(with-organism (:org-id '|ECOLI|) (transcription-unit-all-components '|TU0-8340| ))\n", - "[[u'|G6954|'], [u'|PM0-8720|', u'|EG11346|', u'|BS0-8048|', u'|BS0-8047|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_all_components(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "binding-site-transcription-units\n", - "(binding-site-transcription-units '|BS0-1683| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|BS0-1683| ))\n", - "binding-site-transcription-units\n", - "(binding-site-transcription-units '|BS0-8256| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|BS0-8256| ))\n", - "[[u'|TU0-2021|'], [u'|TU0-13514|']]\n", - "binding-site-transcription-units\n", - "(binding-site-transcription-units '|RBS0-212| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|RBS0-212| ))\n", - "binding-site-transcription-units\n", - "(binding-site-transcription-units '|RBS0-96| )\n", - "(with-organism (:org-id '|ECOLI|) (binding-site-transcription-units '|RBS0-96| ))\n", - "[[u'|TU0-42642|', u'|TU0-42640|', u'|TU0-42638|', u'|TU0-42636|', u'|TU281|', u'|TU00342|'], [u'|TU00392|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_transcription_units(dna_site))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for mrna_site in mrna_sites:\n", - " lst.append(ecoli.binding_site_transcription_units(mrna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15rc1" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/pythoncyc/PTools.py b/pythoncyc/PTools.py index 2b1cb56..8b5a0fe 100644 --- a/pythoncyc/PTools.py +++ b/pythoncyc/PTools.py @@ -194,7 +194,7 @@ def sendQueryToPTools(query): open_socket.close() if isinstance(msg, str) and msg.startswith(':error'): - raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(r)) + raise PToolsError('An internal error occurred in the running Pathway Tools application: {:s}'.format(msg)) else: # Return some result. return msg From 69802f3a01482dbefc73e6a6571547c0cec356ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Mon, 6 Jan 2020 19:26:22 -0300 Subject: [PATCH 10/17] modified setup.py --- README.md | 17 +- .../Operations_on_Compounds-checkpoint.ipynb | 59 ++-- ...ns_on_Enzymatic-Reactions-checkpoint.ipynb | 69 ++--- .../Operations_on_Genes-checkpoint.ipynb | 59 ++-- .../Operations_on_Pathways-checkpoint.ipynb | 59 ++-- ...ins_and_Protein_Complexes-checkpoint.ipynb | 61 ++-- .../Operations_on_Reactions-checkpoint.ipynb | 278 ++++-------------- ...ions_on_Regulation_Frames-checkpoint.ipynb | 59 ++-- .../enumeration_operations-checkpoint.ipynb | 59 ++-- examples/Operations_on_Compounds.ipynb | 59 ++-- .../Operations_on_Enzymatic-Reactions.ipynb | 69 ++--- examples/Operations_on_Genes.ipynb | 59 ++-- examples/Operations_on_Pathways.ipynb | 59 ++-- ...ns_on_Proteins_and_Protein_Complexes.ipynb | 61 ++-- examples/Operations_on_Reactions.ipynb | 278 ++++-------------- .../Operations_on_Regulation_Frames.ipynb | 59 ++-- examples/enumeration_operations.ipynb | 59 ++-- setup.py | 43 ++- 18 files changed, 456 insertions(+), 1010 deletions(-) diff --git a/README.md b/README.md index 6cca8fc..c71baa4 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,19 @@ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +PythonCyc 2.0, January 2020 +=========================== + +Overview +-------- + +An updated version of the original PythonCyc API from Mario Latendresse. + +This module has been testes under Python 3.6 and Python 3.8, with examples +at https://github.com/networkbiolab/PythonCyc/tree/master/examples + +Disclaimer: a number of functions remains broken. + PythonCyc 1.0, November 2014 ============================ @@ -49,13 +62,13 @@ Documentation tutorial.html under the doc directory of this package, or go directly to the tutorial by clicking the following link https://github.com/latendre/PythonCyc/blob/master/doc/tutorial.md -2) For the API documentation of PythonCyc, please consult http://pythoncyc.readthedocs.org. +2) For the API documentation of PythonCyc, please consult http://pythoncyc.readthedocs.org. 3) For the latest news about PythonCyc, please consult http://bioinformatics.ai.sri.com/ptools/pythoncyc.html Author ------- +------ Mario Latendresse, latendre@AI.SRI.COM diff --git a/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb index 8de4802..d4ffabc 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -281,7 +264,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb index 05be910..9b91921 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -204,11 +187,11 @@ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m 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result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." ] } @@ -260,7 +243,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb index 1506a61..418c220 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -600,7 +583,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb index 539ab4f..f47272f 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -389,7 +372,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb index cbe4808..7ed8f93 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", - "\n", - "sys.path" + "\n", + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -935,7 +918,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb index a31329a..1dc2bdb 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -306,11 +289,11 @@ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m 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\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1115\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m 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\u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m 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{:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." ] } @@ -336,20 +319,9 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -368,26 +340,9 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1139\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1140\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1141\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1142\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1143\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." - ] - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -399,20 +354,9 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "specific-rxn\n", @@ -429,20 +373,9 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -452,20 +385,9 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -475,20 +397,9 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -516,25 +427,9 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1240\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCell\u001b[0m \u001b[0mCompartment\u001b[0m \u001b[0mOntology\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1241\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1242\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1244\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" - ] - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -554,29 +449,9 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-PERI-BAC|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-PERI-BAC|']]" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -597,29 +472,9 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|Nucleosides|'],\n", - " ['|D-ALANINE|', '|PROTON|'],\n", - " ['|GUANINE|'],\n", - " ['|DEOXYINOSINE|', '|PROTON|'],\n", - " ['|PROTON|', '|CPD0-2241|'],\n", - " ['|Inorganic-Compounds|'],\n", - " ['|PROTON|', '|D-GALACTURONATE|'],\n", - " ['|CPD0-2486|'],\n", - " ['|MELIBIOSE|', '|LI+|'],\n", - " ['|FORMATE|']]" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -651,20 +506,9 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -681,20 +525,9 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -711,20 +544,9 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, True, False, False, False]" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -756,7 +578,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb index 55f94a3..c9b0d7c 100644 --- a/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -1003,7 +986,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb b/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb index 95419ac..a01d63d 100644 --- a/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb +++ b/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -697,7 +680,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Compounds.ipynb b/examples/Operations_on_Compounds.ipynb index 8de4802..d4ffabc 100644 --- a/examples/Operations_on_Compounds.ipynb +++ b/examples/Operations_on_Compounds.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -281,7 +264,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Enzymatic-Reactions.ipynb b/examples/Operations_on_Enzymatic-Reactions.ipynb index 05be910..9b91921 100644 --- a/examples/Operations_on_Enzymatic-Reactions.ipynb +++ b/examples/Operations_on_Enzymatic-Reactions.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -204,11 +187,11 @@ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." ] } @@ -260,7 +243,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Genes.ipynb b/examples/Operations_on_Genes.ipynb index 1506a61..418c220 100644 --- a/examples/Operations_on_Genes.ipynb +++ b/examples/Operations_on_Genes.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -600,7 +583,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Pathways.ipynb b/examples/Operations_on_Pathways.ipynb index 539ab4f..f47272f 100644 --- a/examples/Operations_on_Pathways.ipynb +++ b/examples/Operations_on_Pathways.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -389,7 +372,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb b/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb index cbe4808..7ed8f93 100644 --- a/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb +++ b/examples/Operations_on_Proteins_and_Protein_Complexes.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", - "\n", - "sys.path" + "\n", + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -935,7 +918,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Reactions.ipynb b/examples/Operations_on_Reactions.ipynb index a31329a..1dc2bdb 100644 --- a/examples/Operations_on_Reactions.ipynb +++ b/examples/Operations_on_Reactions.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -306,11 +289,11 @@ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m 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\u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m 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\u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m 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{:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." ] } @@ -336,20 +319,9 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -368,26 +340,9 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_present_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_present_p\u001b[0;34m(self, rxn, include_spontaneous)\u001b[0m\n\u001b[1;32m 1139\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1140\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1141\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'rxn-present?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1142\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1143\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrxn_specific_form_of_rxn_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecific_rxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeneric_rxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m 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370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'RXN-PRESENT?' is not allowed to be called in restricted mode." - ] - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -399,20 +354,9 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "specific-rxn\n", @@ -429,20 +373,9 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -452,20 +385,9 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -475,20 +397,9 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, False, False, False, False]" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -516,25 +427,9 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompartment_of_rxn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mcompartment_of_rxn\u001b[0;34m(self, rxn, default)\u001b[0m\n\u001b[1;32m 1240\u001b[0m \u001b[0mA\u001b[0m \u001b[0mchild\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCell\u001b[0m \u001b[0mCompartment\u001b[0m \u001b[0mOntology\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1241\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1242\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'compartment-of-rxn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1244\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcompartments_of_reaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msides\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdefault_compartment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m 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"\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/opt/github-repositories/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM\n (:ORG-ID 'ECOLI)\n (COMPARTMENT-OF-RXN\n 'RXN-15348))', the following error occurred: #" - ] - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -554,29 +449,9 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-PERI-BAC|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-CYTOSOL|'],\n", - " ['|CCO-PERI-BAC|']]" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -597,29 +472,9 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|Nucleosides|'],\n", - " ['|D-ALANINE|', '|PROTON|'],\n", - " ['|GUANINE|'],\n", - " ['|DEOXYINOSINE|', '|PROTON|'],\n", - " ['|PROTON|', '|CPD0-2241|'],\n", - " ['|Inorganic-Compounds|'],\n", - " ['|PROTON|', '|D-GALACTURONATE|'],\n", - " ['|CPD0-2486|'],\n", - " ['|MELIBIOSE|', '|LI+|'],\n", - " ['|FORMATE|']]" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -651,20 +506,9 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -681,20 +525,9 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "\"\"\"\n", "rxn\n", @@ -711,20 +544,9 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, False, True, False, False, False]" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "lst = []\n", "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", @@ -756,7 +578,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/Operations_on_Regulation_Frames.ipynb b/examples/Operations_on_Regulation_Frames.ipynb index 55f94a3..c9b0d7c 100644 --- a/examples/Operations_on_Regulation_Frames.ipynb +++ b/examples/Operations_on_Regulation_Frames.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -1003,7 +986,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/examples/enumeration_operations.ipynb b/examples/enumeration_operations.ipynb index 95419ac..a01d63d 100644 --- a/examples/enumeration_operations.ipynb +++ b/examples/enumeration_operations.ipynb @@ -4,57 +4,40 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], - "source": [ - "#to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "import socket\n", - "hostname = socket.gethostname()\n", - "if hostname == \"spica\":\n", - " os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity\n", - "else:\n", - " os.system('nohup /shared/D1/opt/pathway-tools/pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['',\n", - " '/usr/lib/python36.zip',\n", - " '/usr/lib/python3.6',\n", - " '/usr/lib/python3.6/lib-dynload',\n", - " '/home/glucksfall/.local/lib/python3.6/site-packages',\n", - " '/usr/local/lib/python3.6/dist-packages',\n", - " '/usr/lib/python3/dist-packages',\n", - " '/usr/local/lib/python3.6/dist-packages/IPython/extensions',\n", - " '/home/glucksfall/.ipython',\n", - " '/opt/github-repositories/PythonCyc.networkbiolab']" + "0" ] }, - "execution_count": 2, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# modify sys.path to recognize local pythoncyc\n", + "# to run the script, you need to start pathway tools form the command line \n", + "# using the -lisp -python options. Example (from the pathway tools github repository)\n", + "\n", "import os\n", + "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", + "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# modify sys.path to recognize local pythoncyc\n", "import sys\n", - "if hostname == \"spica\":\n", - " path = '/opt/github-repositories'\n", - "else:\n", - " path = '/shared/D1/opt/github-repositories'\n", - "module_path = os.path.abspath(os.path.join(path + '/PythonCyc.networkbiolab/'))\n", - "sys.path.append(module_path)\n", "\n", - "sys.path" + "module_path = os.path.abspath(os.path.join('../'))\n", + "sys.path = [module_path]\n", + "\n", + "# sys.path" ] }, { @@ -697,7 +680,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.6.9" } }, "nbformat": 4, diff --git a/setup.py b/setup.py index 45f8992..ea61da8 100644 --- a/setup.py +++ b/setup.py @@ -20,23 +20,50 @@ # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # ---------------------------------------------------------------------- -# removed distutils because pip cannot uninstall PythonCyc -#from distutils.core import setup +# Always prefer setuptools over distutils from setuptools import setup, find_packages +from codecs import open +from os import path +# include example folder +import glob def main(): - # include other folders in the python packages + # add examples folders + data_files = [] + directories = glob.glob('example/*/*/*') + for directory in directories: + files = glob.glob(directory+'*') + data_files.append((directory, files)) + print(data_files) + + # Get the long description from the README file + here = path.abspath(path.dirname(__file__)) + with open(path.join(here, 'README.md'), encoding='utf-8') as f: + long_description = f.read() setup( name='PythonCyc', + license='SRI International', version='2.0', + description='A Python interface to Pathway Tools, 2019 update', + long_description=long_description, + #long_description_content_type='text/markdown', + url='https://github.com/networkbiolab/PythonCyc', author='Rodrigo Santibáñez', author_email='glucksfall@users.noreply.github.com', - packages=['pythoncyc'], - license='LICENSE', - description='A Python interface to Pathway Tools, 2019 update', - long_description=open('README.md').read() - ) + keywords=[], + packages=find_packages(exclude=['contrib', 'docs', 'tests']), + install_requires=[], + package_data={ + 'example' : ['example'], + }, + data_files=data_files, + project_urls={ + 'Manual': 'https://pythoncyc-v20.readthedocs.io', + 'Bug Reports': 'https://github.com/networkbiolab/PythonCyc/issues', + 'Source': 'https://github.com/networkbiolab/PythonCyc', + }, + ) if __name__ == '__main__': main() From b4a95a20720139557b9f12410586fe9f16d8c070 Mon Sep 17 00:00:00 2001 From: Rodrigo Date: Tue, 7 Jan 2020 00:05:21 -0300 Subject: [PATCH 11/17] updated .gitignore --- .gitignore | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 9fc9476..70755a0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,8 @@ -*pyc +*.pyc __pycache__ +*.egg-info +build/* +dist/* +doc/_build + +.ipynb_checkpoints From aa771e609e04bb601fcb18db32dd5ec5a21014f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Fri, 10 Jan 2020 14:52:24 -0300 Subject: [PATCH 12/17] updated setup.py to include examples in sdist and wheel --- .../Operations_on_Compounds-checkpoint.ipynb | 272 ----- ...ns_on_Enzymatic-Reactions-checkpoint.ipynb | 251 ----- .../Operations_on_Genes-checkpoint.ipynb | 591 ----------- .../Operations_on_Pathways-checkpoint.ipynb | 380 ------- ...ins_and_Protein_Complexes-checkpoint.ipynb | 926 ---------------- .../Operations_on_Reactions-checkpoint.ipynb | 586 ----------- ...ions_on_Regulation_Frames-checkpoint.ipynb | 994 ------------------ .../enumeration_operations-checkpoint.ipynb | 688 ------------ setup.py | 36 +- 9 files changed, 22 insertions(+), 4702 deletions(-) delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb delete mode 100644 examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb diff --git a/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb deleted file mode 100644 index d4ffabc..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Compounds-checkpoint.ipynb +++ /dev/null @@ -1,272 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "\n", - "compounds = [x.frameid for x in ecoli.compounds.instances][0:2]\n", - "reactions = [x.frameid for x in ecoli.reactions.instances][0:2]\n", - "enzymes = ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|RXN0-5298|'], ['|RXN0-1922|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "cpd\n", - "A child of class |Compounds|. \n", - "non-specific-too?\n", - "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", - "parent of cpd, appears as a substrate. \n", - "transport-only?\n", - "Keyword, Optional If non-nil, return only transport reactions. \n", - "compartment\n", - "Keyword, Optional If non-nil, return only reactions within the specified \n", - "compartment. \n", - "enzymatic?\n", - "Keyword, Optional If non-nil, return only enzymatic reactions. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for compound in compounds:\n", - " lst.append(ecoli.reactions_of_compound(compound, enzymatic = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for compound in compounds:\n", - " for reaction in reactions:\n", - " lst.append(ecoli.substrate_of_generic_rxn(compound, reaction))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|FUCCAT-PWY|', '|FUC-RHAMCAT-PWY|'], []]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "cpd\n", - "An instance of class |Compounds|. \n", - "non-specific-too?\n", - "Keyword, Optional If non-nil, returns all generic reactions where cpd, or a \n", - "parent of cpd, appears as a substrate. \n", - "modulators?\n", - "Keyword, Optional If non-nil, returns pathways where cpd appears as a regulator \n", - "as well. \n", - "phys-relevant?\n", - "Keyword, Optional If true, then only return inhibitors that are associated with \n", - "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", - "non-nil. \n", - "include-rxns?\n", - "Keyword, Optional If non-nil, then return a list of reaction-pathway pairs. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for compound in compounds:\n", - " lst.append(ecoli.pathways_of_compound(compound))#, modulators = True, include_rxns = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "cpds\n", - "An instance or list of instances of class |Compounds|. \n", - "mode\n", - "Keyword, Optional Represents the type of regulation. Can take on the values of \n", - "“+”, “-”, or 'nil. \n", - "mechanisms\n", - "Keyword, Optional Keywords from the 'mechanism slot of the corresponding \n", - "sub-class of the class |Regulation|. If non-nil, only regulation objects with \n", - "mechanisms in this list will be explored for regulated objects. \n", - "phys-relevant?\n", - "Keyword, Optional If true, then only return inhibitors that are associated with \n", - "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", - "non-nil. \n", - "slots\n", - "Keyword A list of enzymatic reaction slots to \n", - "\"\"\"\n", - "\n", - "try:\n", - " lst = []\n", - " for compound in compounds:\n", - " lst.append(ecoli.activated_or_inhibited_by_compound(compound))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for compound in compounds:\n", - " lst.append(ecoli.tfs_bound_to_compound(compound, include_inactive = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['dsbd-rxn', 'rxn0-4342']\n", - "['4-hydroxy-2-oxovalerate aldolase', 'L,D-transpeptidase YcfS']\n" - ] - } - ], - "source": [ - "# Object Name Manipulation Operations\n", - "# lst = []\n", - "# for reaction in reactions:\n", - "# lst.append(ecoli.get_name_string(reaction))\n", - "# print lst[-10:]\n", - "# print ''\n", - "\n", - "lst = []\n", - "for reaction in reactions:\n", - " lst.append(ecoli.full_enzyme_name(reaction))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for enzyme in enzymes:\n", - " lst.append(ecoli.enzyme_activity_name(enzyme))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb deleted file mode 100644 index 9b91921..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Enzymatic-Reactions-checkpoint.ipynb +++ /dev/null @@ -1,251 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = 'all'):\n", - " lst.append(ecoli.cofactors_and_pgroups_of_enzrxn(enzrxn = enzrxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "er\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "phys-relevant-only?\n", - "Optional If true, then only return activators that are associated with \n", - "|Regulation| instances that have the 'physiologically‑relevant? slot set to \n", - "non-nil. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.enzrxn_activators(enzrxn = enzrxn, phys_relevant_only=True))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.enzrxn_inhibitors(enzrxn = enzrxn, phys_relevant_only = True))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[], [], [], [], [], [], [], [], [], []]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "enzrxn\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "include-super-pwys?\n", - "Keyword, Optional If non-nil, then not only will the direct pathways in which \n", - "enzrxn is associated in be returned, but also any enclosing super-pathways. If \n", - "enzrxn is associated with a reaction that is directly associated with a \n", - "super-pathway, then the function might return super-pathways even if this option \n", - "is nil.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for enzrxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.pathways_of_enzrxn(enzrxn = enzrxn, include_super_pwys = False))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn2\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'metab-smm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n\u001b[0;32m---> 19\u001b[0;31m pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n\u001b[0m\u001b[1;32m 20\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mpathway_allows_enzrxn\u001b[0;34m(self, pwy, rxn, enzrxn, single_species)\u001b[0m\n\u001b[1;32m 1644\u001b[0m \u001b[0;31m# single_species is optional for the Lisp version.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1645\u001b[0m \u001b[0;31m# TODO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1646\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pathway-allows-enzrxn?'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpwy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0menzrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msingle_species\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1647\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1648\u001b[0m \u001b[0;31m# Section 5.1.4 Operations on Proteins\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'PATHWAY-ALLOWS-ENZRXN?' is not allowed to be called in restricted mode." - ] - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "enzrxn\n", - "An instance of the class |Enzymatic‑Reactions|. \n", - "single-species\n", - "Optional An instance of the class |Organisms| If set, then enzrxn has the \n", - "further stricture that it must be an enzymatic reaction present in the organism \n", - "specified by the value passed to single‑species.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " for rxn1 in ecoli.all_rxns(type_of_reactions = 'all'):\n", - " for rxn2 in ecoli.all_rxns(type_of_reactions = 'metab-smm'):\n", - " lst.append([rxn1, rxn2, ecoli.pathway_allows_enzrxn(\n", - " pwy = pwy, rxn = rxn1, enzrxn = rxn2, single_species = u'|ECOLI|')])\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb deleted file mode 100644 index 418c220..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Genes-checkpoint.ipynb +++ /dev/null @@ -1,591 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "genes = [x.frameid for x in ecoli.genes.instances][0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|Genes|', '|Genes|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.gene_p(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.enzymes_of_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|EG11414-MONOMER|', '|CPLX0-7910|', '|CPLX0-3803|'], ['|EG11127-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.all_products_of_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.reactions_of_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.pathways_of_gene(gene, True, True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|COLI-K12|', '|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.chromosome_of_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|EG11414-MONOMER|', '|EG11127-MONOMER|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.unmodified_gene_product(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|EG11414-MONOMER|'], ['|EG11127-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.unmodified_gene_products(gene = gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|EG10850|', '|EG11024|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.next_gene_on_replicon(gene = gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|G7950|', '|EG11126|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.previous_gene_on_replicon(gene = gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "both queries are the same.\n", - "both queries are the same.\n", - "[None, False, False, None]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene1 in genes:\n", - " for gene2 in genes:\n", - " lst.append(ecoli.adjacent_genes_p(gene1, gene2))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "both queries are the same.\n", - "both queries are the same.\n", - "[None, False, False, None]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene1 in genes:\n", - " for gene2 in genes:\n", - " lst.append(ecoli.neighboring_genes_p(gene1, gene2))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'|EG11127|': ['|EG11414|']}" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.gene_clusters(genes, 4000)" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for gene in genes:\n", - " lst.append(ecoli.rna_coding_gene(gene=gene))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for gene in genes:\n", - " lst.append(ecoli.protein_coding_gene(gene=gene))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.pseudo_gene_p(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.phantom_gene_p(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.dna_binding_site_p(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.terminator_p(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-36411|', '|TU0-13193|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.operon_of_gene(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|EG12115|', '|EG10850|', '|EG11414|'], ['|EG11125|', '|EG11126|', '|EG11127|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.genes_in_same_operon(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.gene_transcription_units(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|EG12115|', '|EG10850|'], ['|EG11125|', '|EG11126|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.cotranscribed_genes(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.terminators_affecting_gene(gene=gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|COLI-K12|', '|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.chromosome_of_object(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb deleted file mode 100644 index f47272f..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Pathways-checkpoint.ipynb +++ /dev/null @@ -1,380 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|EG12082|',\n", - " '|EG12088|',\n", - " '|EG12090|',\n", - " '|EG12091|',\n", - " '|EG12092|',\n", - " '|EG11773|',\n", - " '|EG12093|',\n", - " '|EG12089|',\n", - " '|EG12087|',\n", - " '|EG11774|',\n", - " '|EG12086|',\n", - " '|EG12084|',\n", - " '|EG12083|',\n", - " '|EG10330|',\n", - " '|EG10331|',\n", - " '|EG10332|',\n", - " '|EG10333|']" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "sorted?\n", - "Keyword, Optional If true, the genes are sorted in the order in which the \n", - "corresponding reaction occurrs in the sequence of the pathway. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = 'all', base = True):\n", - " lst.append(ecoli.genes_of_pathway(pwy = pwy, sorted = True))\n", - "lst[-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|NADH-DHI-CPLX|', '|FUMARATE-REDUCTASE|']" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "species\n", - "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", - "MetaCyc, only proteins found in those organisms will be returned. This list can \n", - "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", - "the documentation for the 'species slot‑unit for more information. \n", - "experimental-only?\n", - "Keyword, Optional When true, only return enzymes that have a non-computational \n", - "evidence code associated with it. \n", - "sorted?\n", - "Keyword, Optional If true, the enzymes are sorted in the order in which the \n", - "corresponding reaction occurrs in the sequence of the pathway. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.enzymes_of_pathway(pwy = pwy, sorted = True, experimental_only = True))\n", - "lst[-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|FUM|',\n", - " '|SUC|',\n", - " '|Menaquinones|',\n", - " '|Menaquinols|',\n", - " '|E-|',\n", - " '|PROTON|',\n", - " '|NAD|',\n", - " '|NADH|']" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.compounds_of_pathway(pwy = pwy))\n", - "lst[-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|NADH|',\n", - " '|Menaquinones|',\n", - " '|Menaquinols|',\n", - " '|PROTON|',\n", - " '|TRIMETHYLAMINE-N-O|'],\n", - " ['|TRIMETHYLAMINE-N-O|', '|NADH|'],\n", - " ['|NAD|',\n", - " '|Menaquinols|',\n", - " '|PROTON|',\n", - " '|TRIMETHYLAMINE|',\n", - " '|WATER|',\n", - " '|Menaquinones|'],\n", - " ['|WATER|', '|TRIMETHYLAMINE|', '|NAD|']]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.substrates_of_pathway(pwy = pwy))\n", - "lst[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[],\n", - " ['|PWY-7195|', '|PWY-6556|'],\n", - " ['|PWY0-1597|'],\n", - " ['|RIBOSYN2-PWY|'],\n", - " ['|PWY0-1295|', '|PWY-6556|'],\n", - " [],\n", - " ['|PWY0-1584|', '|PWY0-1581|', '|PWY0-1573|', '|PWY0-1352|'],\n", - " [],\n", - " [],\n", - " []]" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.variants_of_pathway(pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[['|RXN0-5264|', '|RXN0-5388|']], 1, 2, 2]" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "pwy\n", - "An instance of the class |Pathways|, which is not a super-pathway (i.e., does \n", - "not have any entries in its 'sub‑pathways slot). \n", - "rxn-list\n", - "Optional The list of reactions to use as the starting list of connected \n", - "component clusters. Defaults to (get‑slot‑values pwy 'reaction‑list).\n", - "\n", - "pred-list\n", - "Optional The list of reaction predecessors to iterate from in order to cluster \n", - "the reactions in rxn‑list. Defaults to (get‑slot‑values pwy 'predecessors).\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.pathway_components(pwy = pwy))\n", - "lst[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[False, False, False, False, False, True, False, True, False, False]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True):\n", - " lst.append(ecoli.noncontiguous_pathway_p(pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|DMKCYT-RXN|', '|RXN-15348|', False],\n", - " ['|DMKCYT-RXN|', '|LACTALDREDUCT-RXN|', False],\n", - " ['|DMKCYT-RXN|', '|PFLDEACTIV-RXN|', False],\n", - " ['|DMKCYT-RXN|', '|OHMETPYRKIN-RXN|', False],\n", - " ['|DMKCYT-RXN|', '|RXN0-7094|', False],\n", - " ['|DMKCYT-RXN|', '|TRIOSEPISOMERIZATION-RXN|', False],\n", - " ['|DMKCYT-RXN|', '|RXN0-7298|', False],\n", - " ['|DMKCYT-RXN|', '|RXN0-1137|', False],\n", - " ['|DMKCYT-RXN|', '|BADH-RXN|', False],\n", - " ['|DMKCYT-RXN|', '|DMKCYT-RXN|', False]]" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn1\n", - "An instance of the class |Reactions|. \n", - "rxn2\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "An instance of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for pwy in ecoli.all_pathways(selector = ':all', base = True)[0:10]:\n", - " for rxn1 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", - " for rxn2 in ecoli.all_rxns(type_of_reactions = ':all')[0:10]:\n", - " lst.append([rxn1, rxn2, ecoli.rxns_adjacent_in_pwy_p(rxn1 = rxn1, rxn2 = rxn2, pwy = pwy)])\n", - "# lst.append(ecoli.rxns_adjacent_in_pwy_p(rxn1 = u'|RXN0-5264|', rxn2 = u'|RXN0-5388|', pwy = pwy))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb deleted file mode 100644 index 7ed8f93..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Proteins_and_Protein_Complexes-checkpoint.ipynb +++ /dev/null @@ -1,926 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", - "complexes = ecoli.all_protein_complexes()[0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", - "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "coefficients?\n", - "Keyword, Optional If true, then the second return value of the function will be \n", - "a list of monomer coefficients. Defaults to true. \n", - "unmodify?\n", - "Keyword, Optional If true, obtain the monomers of the unmodified form of p.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.monomers_of_protein(protein = protein, coefficients = True, unmodify = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.monomers_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[['|G6106-MONOMER|'], [4]], [['|URAA-MONOMER|'], [2]]]\n", - "[[['|OPPC-MONOMER|'], [1]], [['|YHBN-MONOMER|'], [1]]]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "exclude-small-molecules?\n", - "Keyword, Optional If nil, then small molecule components are also returned. \n", - "Default value is true. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.base_components_of_protein(protein = protein, exclude_small_molecules = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.base_components_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n", - "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.containers_of(protein = protein, exclude_self = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_or_rna_containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "exclude-self?\n", - "Optional If true, then protein will not be included in the return value. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.homomultimeric_containers_of(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[True, True]\n", - "[True, True]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.polypeptide_or_homomultimer_p(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|CPLX0-7660|', '|CPLX0-8247|']\n", - "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.unmodified_form(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.unmodified_form(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|CPLX0-7660|', '|CPLX0-8247|']\n", - "['|OPPC-MONOMER|', '|YHBN-MONOMER|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.unmodified_or_unbound_form(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "prots\n", - "A list of instances of the class |Proteins|. \n", - "debind?\n", - "Keyword, Optional When non-nil, the proteins are further simplified by obtaining \n", - "the unbound form of the protein, if it is bound to a small molecule. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reduce_modified_proteins(prots = [protein], debind = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reduce_modified_proteins(prots = [protein]))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.all_direct_forms_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6106-MONOMER|', '|CPLX0-7660|'], ['|URAA-MONOMER|', '|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.all_forms_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n", - "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_forms(protein = protein, all_variants = True, exclude_self= True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_forms(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|'], ['|YHBN-MONOMER|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_and_unmodified_forms(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|OPPC-MONOMER|', '|CPLX0-3970|', '|ABC-22-CPLX|'], ['|YHBN-MONOMER|', '|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.modified_containers(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.modified_containers(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|CPLX0-7660|'], ['|CPLX0-8247|']]\n", - "[['|CPLX0-3970|', '|ABC-22-CPLX|'], ['|CPLX0-7992|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.top_containers(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.top_containers(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.small_molecule_cplxes_of_prot(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6106|'], ['|EG12129|']]\n", - "[['|EG10676|'], ['|G7665|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.genes_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6106|'], ['|EG12129|']]\n", - "[['|EG10676|'], ['|G7665|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.genes_of_proteins(prots = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_of_proteins(prots = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", - "[[], []]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "protein\n", - "An instance of the class |Proteins|. \n", - "kb\n", - "Keyword, Optional The KB object of the KB in which to find the associated \n", - "reactions. Defaults to the current PGDB. \n", - "include-specific-forms?\n", - "Keyword, Optional When true, specific forms of associated generic reactions are \n", - "also returned. Default value is true. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reactions_of_enzyme(protein = protein, include_subreactions = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reactions_of_enzyme(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|ECOLI|'], ['|ECOLI|']]\n", - "[['|ECOLI|'], ['|ECOLI|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.species_of_protein(protein = protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.species_of_protein(protein = protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[True, True]\n", - "[False, False]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "type\n", - "Optional Can take on one of the following values to select more precisely what \n", - "is meant by an “enzyme”:\n", - "\n", - ":any\n", - "Any protein that catalyzes a reaction is considered an enzyme. \n", - ":chemical-change\n", - "If the reactants and products of the catalyzed reactin differ, and not just by \n", - "their cellular location, then the protein is considered an enzyme. \n", - ":small-molecule\n", - "If the reactants of the catalyzed reaction differ and are small molecules, then \n", - "the protein is considered an enzyme. \n", - ":transport\n", - "If the protein catalyzes a transport reaction. \n", - ":non-transport\n", - "If the protein only catalyzes non-transport reactions. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'any'))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.enzyme_p(protein = protein, type_of_reactions = 'non-transport-non-pathway'))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for protein in complexes:\n", - " lst.append(ecoli.leader_peptide_p(protein = protein))\n", - " print(lst[-10:])\n", - "\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.leader_peptide_p(protein = protein))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|Proteins|', '|Proteins|']\n", - "['|Proteins|', '|Proteins|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_p(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_p(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|Protein-Complexes|', '|Protein-Complexes|']\n", - "[False, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.complex_p(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.complex_p(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|RXN0-4301|'], ['|TRANS-RXN-132|']]\n", - "[[], []]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "p\n", - "An instance of the class |Proteins|. \n", - "check-protein-components?\n", - "Optional If true, check all components of this protein for catalyzed reactions. \n", - "Defaults to true. \n", - "check-protein-containers?\n", - "Optional If true, check the containers and modified forms of the protein for \n", - "catalyzed reactions. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_containers = True))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.reactions_of_protein(protein = protein, check_protein_components = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, False]\n", - "['|CCI-CYTOSOL-GN|', False]\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "compartments\n", - "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", - "See frame 'CCO. \n", - "default-ok?\n", - "Keyword, Optional If true, then we return true if the reaction has no associated \n", - "compartment information, or one of its associated locations is a super-class of \n", - "one of the members of the compartments argument. \n", - "pwy\n", - "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", - "rxn is limited to the given child of |Pathways|. \n", - "loose?\n", - "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", - "are treated as being the same compartment. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = 'CCO-CYTOSOL'))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.protein_in_compartment_p(rxn = protein, compartments = ['CCO-CYTOSOL', 'CCO-MEMBRANE']))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|MTR-MONOMER|', '|G7942-MONOMER|', '|NANT-MONOMER|', '|B1006-MONOMER|', '|YDHE-MONOMER|', '|YDEA-MONOMER|', '|PITA-MONOMER|', '|YEIM-MONOMER|', '|BCR-MONOMER|', '|YGFO-MONOMER|']\n" - ] - } - ], - "source": [ - "\"\"\"\n", - "membranes\n", - "Keyword Either :all or a list of instances of the class. Defaults to :all \n", - "'CCO‑MEMBRANE. \n", - "method\n", - "Either :location or :reaction‑compartments. :location will check the 'locations \n", - "slot, while :reaction‑compartments will examine the compartments of reaction \n", - "substrates. Default value is :location. \n", - "\"\"\"\n", - "\n", - "lst = ecoli.all_transporters_across(membranes = 'all')\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n", - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in complexes:\n", - " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.autocatalytic_reactions_of_enzyme(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb deleted file mode 100644 index 1dc2bdb..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Reactions-checkpoint.ipynb +++ /dev/null @@ -1,586 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|G6350|'],\n", - " ['|EG10754|'],\n", - " [],\n", - " [],\n", - " [],\n", - " ['|EG10068|'],\n", - " ['|EG10278|', '|G7213|'],\n", - " [],\n", - " ['|G7590|'],\n", - " []]" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.genes_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|NICOTINATE_NUCLEOTIDE|', '|ATP|', '|PROTON|', '|PPI|', '|DEAMIDO-NAD|'],\n", - " ['|ACETALD|', '|PYRUVATE|', '|PROTON|', '|ACETOIN|', '|CARBON-DIOXIDE|'],\n", - " ['|Protein-Red-Disulfides|',\n", - " '|MONOMER0-4152|',\n", - " '|MONOMER0-4438|',\n", - " '|Protein-Ox-Disulfides|'],\n", - " ['|PROTON|', '|AMINO-OXOBUT|', '|AMINO-ACETONE|', '|CARBON-DIOXIDE|'],\n", - " ['|Cytochromes-B-Reduced|', '|Cytochromes-B|', '|Reduced-Cytochromes-o|'],\n", - " ['|ATP|',\n", - " '|L-CITRULLINE|',\n", - " '|L-ASPARTATE|',\n", - " '|PROTON|',\n", - " '|L-ARGININO-SUCCINATE|',\n", - " '|PPI|',\n", - " '|AMP|'],\n", - " ['|ACETYL-COA|', '|CPD-7221|', '|CPD-15244|', '|CO-A|'],\n", - " ['|MONOMER0-1641|', '|TORR-CPLX|', '|CPLX0-2821|'],\n", - " ['|ATP|',\n", - " '|D-BETA-D-HEPTOSE-1-P|',\n", - " '|PROTON|',\n", - " '|ADP-D-GLYCERO-D-MANNO-HEPTOSE|',\n", - " '|PPI|'],\n", - " ['|DSBD-MONOMER|', '|CPLX0-8004|', '|DSBG-MONOMER|', '|DSBDOXI-MONOMER|']]" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.substrates_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|NICONUCADENYLYLTRAN-MONOMER|'],\n", - " ['|PYRUVOXID-CPLX|'],\n", - " [],\n", - " [],\n", - " [],\n", - " ['|CPLX0-238|'],\n", - " ['|G7213-MONOMER|', '|FADA-CPLX|'],\n", - " [],\n", - " ['|CPLX0-3661|'],\n", - " []]" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "species\n", - "Keyword, Optional A list of species, such that in a multi-organism PGDB such as \n", - "MetaCyc, only proteins found in those organisms will be returned. This list can \n", - "include valid org‑ids, children of class |Organisms|, and strings. Please see \n", - "the documentation for the 'species slot‑unit for more information. Default value \n", - "is nil. \n", - "experimental-only?\n", - "Keyword, Optional When true, only return enzymes that have a non-computational \n", - "evidence code associated with it. \n", - "local-only-p\n", - "Keyword, Optional When true, only return enzymes that catalyze the specific form \n", - "of the reaction, as opposed to enzymes that are known to catalyze a more general \n", - "form (i.e., class) of the reaction. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.enzymes_of_reaction(rxn = rxn, species = u'|ECOLI|', \n", - " experimental_only = False, local_only_p = False))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[[['|PROTON|', '|ATP|', '|NICOTINATE_NUCLEOTIDE|'],\n", - " ['|PPI|', '|DEAMIDO-NAD|']],\n", - " [['|PROTON|', '|PYRUVATE|', '|ACETALD|'], ['|ACETOIN|', '|CARBON-DIOXIDE|']],\n", - " [['|MONOMER0-4152|', '|Protein-Red-Disulfides|'],\n", - " ['|MONOMER0-4438|', '|Protein-Ox-Disulfides|']],\n", - " [['|AMINO-OXOBUT|', '|PROTON|'], ['|AMINO-ACETONE|', '|CARBON-DIOXIDE|']],\n", - " [['|Cytochromes-B-Reduced|', '|Cytochromes-B|'],\n", - " ['|Cytochromes-B|', '|Reduced-Cytochromes-o|']],\n", - " [['|L-ASPARTATE|', '|L-CITRULLINE|', '|ATP|'],\n", - " ['|PROTON|', '|L-ARGININO-SUCCINATE|', '|PPI|', '|AMP|']],\n", - " [['|CPD-15244|', '|CO-A|'], ['|CPD-7221|', '|ACETYL-COA|']],\n", - " None,\n", - " [['|PROTON|', '|D-BETA-D-HEPTOSE-1-P|', '|ATP|'],\n", - " ['|ADP-D-GLYCERO-D-MANNO-HEPTOSE|', '|PPI|']],\n", - " None]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "direction\n", - "Keyword, Optional Can take on the following values:\n", - "\n", - ":L2R\n", - "The reaction direction goes from ‘left to right’, as described in the \n", - "|Reactions| instance. \n", - ":R2L\n", - "The reaction direction goes from ‘right to left’; the opposite of what is \n", - "described in the |Reactions| instance. \n", - "\n", - "pwy\n", - "Keyword, Optional An instance of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.reaction_reactants_and_products(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|SMALL-MOLECULE|',\n", - " '|SMALL-MOLECULE|',\n", - " '|PROTEIN-REACTION|',\n", - " '|SMALL-MOLECULE|',\n", - " '|PROTEIN-REACTION|',\n", - " '|SMALL-MOLECULE|',\n", - " '|SMALL-MOLECULE|',\n", - " '|PROTEIN-REACTION|',\n", - " '|SMALL-MOLECULE|',\n", - " '|PROTEIN-REACTION|']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.reaction_type(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "ename": "PToolsError", - "evalue": "An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mPToolsError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mlst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mrxn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall_rxns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype_of_reactions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':all'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0mlst\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecoli\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxn_without_sequenced_enzyme_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0mlst\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36mrxn_without_sequenced_enzyme_p\u001b[0;34m(self, rxn)\u001b[0m\n\u001b[1;32m 1111\u001b[0m \u001b[0mA\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1112\u001b[0m \t\t\"\"\"\n\u001b[0;32m-> 1113\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'reaction-without-sequenced-enzyme-p'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmay_be_frameid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1115\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mpathway_hole_p\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrxn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCallBool\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mThis\u001b[0m \u001b[0mmethod\u001b[0m \u001b[0mtakes\u001b[0m \u001b[0mcare\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtranslating\u001b[0m \u001b[0mno\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0man\u001b[0m \u001b[0mempty\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mto\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \t\t\"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbFnCall\u001b[0;34m(self, fn, *args, **kwargs)\u001b[0m\n\u001b[1;32m 370\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 371\u001b[0m \u001b[0mfnCall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprepareFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 372\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendPgdbQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfnCall\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 373\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 374\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCallBool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PGDB.py\u001b[0m in \u001b[0;36msendPgdbQuery\u001b[0;34m(self, query)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpythoncyc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_debug\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 360\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 361\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mPTools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msendQueryToPTools\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlisp_query\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 362\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 363\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msendPgdbFnCall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/shared/D1/opt/repositories/git-reps/PythonCyc.networkbiolab/pythoncyc/PTools.py\u001b[0m in \u001b[0;36msendQueryToPTools\u001b[0;34m(query)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 196\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m':error'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 197\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mPToolsError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'An internal error occurred in the running Pathway Tools application: {:s}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 198\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m# Return some result.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mPToolsError\u001b[0m: An internal error occurred in the running Pathway Tools application: :error, The function 'REACTION-WITHOUT-SEQUENCED-ENZYME-P' is not allowed to be called in restricted mode." - ] - } - ], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "complete?\n", - "Optional If true, the predicate will return true when there is any associated \n", - "gene without a sequence. If nil, the predicate will return true when all \n", - "associated genes are without a sequence. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.rxn_without_sequenced_enzyme_p(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is REACTION-WITHOUT-SEQUENCED-ENZYME-P, \n", - "# which only argument is a rxn" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "hole-if-any-gene-without-position?\n", - "Keyword, Optional If true, then genes without specified coordinates for the \n", - "current organism’s genome are not counted when determining the status of the \n", - "reaction.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.pathway_hole_p(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.rxn_present_p(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is RXN-PRESENT?" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "specific-rxn\n", - "A child of the class |Reactions|. \n", - "generic-rxn\n", - "A child of the class |Reactions|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.rxn_specific_form_of_rxn_p(specific_rxn = rxn, generic_rxn = u'|RXN0-3741|'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.nonspecific_forms_of_rxn(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.specific_forms_of_rxn(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "compartments\n", - "A list of cellular compartments, as defined in the Cellular Components Ontology. \n", - "See frame 'CCO. \n", - "default-ok?\n", - "Keyword, Optional If true, then we return true if the reaction has no associated \n", - "compartment information, or one of its associated locations is a super-class of \n", - "one of the members of the compartments argument. \n", - "pwy\n", - "Keyword, Optional If supplied, the search for associated enzymes of the argument \n", - "rxn is limited to the given child of |Pathways|. \n", - "loose?\n", - "Keyword, Optional If true, then the compartments 'CCO‑CYTOPLASM and 'CCO‑CYTOSOL \n", - "are treated as being the same compartment.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.rxn_in_compartment_p(rxn = rxn, compartments = [u'|CCO_CYTOSOL|']))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "default\n", - "Optional The default compartment for reactions without any compartment \n", - "annotations on their substrates. The default value is 'CCO‑CYTOSOL. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.compartment_of_rxn(rxn = rxn))\n", - "lst[-10:]\n", - "\n", - "# this raise an error because the lisp function is missing (?)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "sides\n", - "Keyword, Optional The slots of the reaction to consider. The default value is \n", - "'(LEFT RIGHT). \n", - "default-compartment\n", - "The default compartment, as determined by the function (default‑compartment), \n", - "which currently is set to 'CCO‑CYTOSOL.\n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.compartments_of_reaction(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "side\n", - "Keyword, Optional The side of the reaction from which to return the transported \n", - "compound. \n", - "primary-only?\n", - "Keyword, Optional If true, then filter out common exchangers (currently defined \n", - "as '(PROTON NA CPD-1)+). If true, and the only transported compounds are in this \n", - "list, then the filter doesn’t apply. \n", - "from-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", - "return compounds transported from that compartment. \n", - "to-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, then only \n", - "return compounds transported to that compartment. \n", - "show-compartment\n", - "Keyword, Optional A compartment (child of class 'CCO). If specified, and the \n", - "compound is modified during transport, then only return the form of the compound \n", - "as found in this compartment. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':transport'):\n", - " lst.append(ecoli.transported_chemicals(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "A child of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.get_predecessors(rxn = rxn, pwy = u'PWY0-1347'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\"\"\"\n", - "rxn\n", - "An instance of the class |Reactions|. \n", - "pwy\n", - "A child of the class |Pathways|. \n", - "\"\"\"\n", - "\n", - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.get_successors(rxn = rxn, pwy = u'PWY0-1347'))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "lst = []\n", - "for rxn in ecoli.all_rxns(type_of_reactions = ':all'):\n", - " lst.append(ecoli.rxn_w_isozymes_p(rxn = rxn))\n", - "lst[-10:]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb b/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb deleted file mode 100644 index c9b0d7c..0000000 --- a/examples/.ipynb_checkpoints/Operations_on_Regulation_Frames-checkpoint.ipynb +++ /dev/null @@ -1,994 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')\n", - "\n", - "regs = [x.frameid for x in ecoli.regulation.instances][0:2]\n", - "genes = [x.frameid for x in ecoli.genes.instances][0:2]\n", - "proteins = [x.frameid for x in ecoli.proteins.instances][0:2]\n", - "tus = [x.frameid for x in ecoli.transcription_units.instances][0:2]\n", - "dna_sites = [x.frameid for x in ecoli.DNA_Binding_Sites.instances][0:2]\n", - "mrna_sites = [x.frameid for x in ecoli.mRNA_Binding_Sites.instances][0:2]\n", - "terminators = [x.frameid for x in ecoli.Terminators.instances][0:2]\n", - "promoters = [x.frameid for x in ecoli.Promoters.instances][0:2]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[True, False]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.activation_p(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[False, True]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.inhibition_p(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_regulators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_activators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.direct_inhibitors(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_p(protein))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.regulator_of_type(protein, class_name = ':activator'))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.regulon_of_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU162|'], ['|TU461|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for reg in regs:\n", - " lst.append(ecoli.regulation_frame_transcription_units(reg))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|REG0-11053|', '|REG0-11052|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_regulation_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_activation_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|REG0-11053|', '|REG0-11052|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_inhibition_frames(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.transcription_units_of_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.genes_regulated_by_protein(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.DNA_binding_sites_of_protein(protein, all_forms = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.regulator_proteins_of_transcription_unit(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [], - "source": [ - "try:\n", - " lst = []\n", - " for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_ligands(protein, u':both'))\n", - " print(lst[-10:])\n", - "except:\n", - " pass" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for protein in proteins:\n", - " lst.append(ecoli.transcription_factor_active_forms(protein))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|G6761|', '|EG10457|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.genes_regulating_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.genes_regulated_by_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[None, None, None], [['|G6761-MONOMER|'], ['|PD00288|'], None]]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.regulators_of_gene_transcription(gene, by_function = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_activators(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_inhibitors(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[None, None, None], [None, ['|PD01379|'], None]]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.regulators_of_operon_transcription(tu, by_function = True))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[None, '|PM0-8720|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_promoter(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6954|'], ['|EG11346|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_genes(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|G6954|', '|EG11346|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_first_gene(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|BS0-8048|', '|BS0-8047|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_binding_sites(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|PD01379|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_transcription_factors(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 33, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_mrna_binding_sites(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 34, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|COLI-K12|', '|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.chromosome_of_operon(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], ['|BS0-7937|', '|BS0-7936|', '|BS0-7935|', '|BS0-7225|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.binding_sites_affecting_gene(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for gene in genes:\n", - " lst.append(ecoli.binding_site_to_regulators(gene))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|PHOSPHO-PHOB|'], ['|CPLX0-7639|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_to_regulators(dna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 38, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU0-13975|'], ['|TU0-8636|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for promoter in promoters:\n", - " lst.append(ecoli.transcription_units_of_promoter(promoter))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for promoter in promoters:\n", - " lst.append(ecoli.promoter_binding_sites(promoter))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[], []]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_terminators(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 41, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU0-8814|'], ['|TU0-8340|']]\n", - "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n", - "[['|TU0-2021|'], ['|TU0-13514|']]\n", - "[['|TU0-13975|'], ['|TU0-8636|']]\n", - "[['|TU0-14216|'], ['|TU0-36408|', '|TU0-13193|']]\n", - "[['|TU-8390|', '|TU-8389|'], ['|TU00091|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in mrna_sites:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in dna_sites:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in promoters:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in genes:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in terminators:\n", - " lst.append(ecoli.containing_tus(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|COLI-K12|', '|COLI-K12|']\n", - "['|COLI-K12|', '|COLI-K12|']\n", - "['|COLI-K12|', '|COLI-K12|']\n", - "['|COLI-K12|', '|COLI-K12|']\n", - "['|COLI-K12|', '|COLI-K12|']\n", - "['|COLI-K12|', '|COLI-K12|']\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in mrna_sites:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in dna_sites:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in promoters:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in genes:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for tu in terminators:\n", - " lst.append(ecoli.containing_chromosome(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|PM0-2201|'], ['|PM0-9620|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_promoters(dna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|G6954|'], ['|PM0-8720|', '|EG11346|', '|BS0-8048|', '|BS0-8047|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for tu in tus:\n", - " lst.append(ecoli.transcription_unit_all_components(tu))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[['|TU0-2021|'], ['|TU0-13514|']]\n", - "[['|TU0-42642|', '|TU0-42640|', '|TU0-42638|', '|TU0-42636|', '|TU281|', '|TU00342|'], ['|TU00392|']]\n" - ] - } - ], - "source": [ - "lst = []\n", - "for dna_site in dna_sites:\n", - " lst.append(ecoli.binding_site_transcription_units(dna_site))\n", - "print(lst[-10:])\n", - "\n", - "lst = []\n", - "for mrna_site in mrna_sites:\n", - " lst.append(ecoli.binding_site_transcription_units(mrna_site))\n", - "print(lst[-10:])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb b/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb deleted file mode 100644 index a01d63d..0000000 --- a/examples/.ipynb_checkpoints/enumeration_operations-checkpoint.ipynb +++ /dev/null @@ -1,688 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# to run the script, you need to start pathway tools form the command line \n", - "# using the -lisp -python options. Example (from the pathway tools github repository)\n", - "\n", - "import os\n", - "# os.system('nohup /opt/pathway-tools/pathway-tools -lisp -python &')\n", - "os.system('nohup pathway-tools -lisp -python-local-only &') # added cybersecurity" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# modify sys.path to recognize local pythoncyc\n", - "import sys\n", - "\n", - "module_path = os.path.abspath(os.path.join('../'))\n", - "sys.path = [module_path]\n", - "\n", - "# sys.path" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|META|', '|ECOLI|']\n" - ] - } - ], - "source": [ - "import pythoncyc\n", - "all_orgids = pythoncyc.all_orgids()\n", - "print(all_orgids)\n", - "\n", - "meta = pythoncyc.select_organism(u'|META|')\n", - "ecoli = pythoncyc.select_organism(u'|ECOLI|')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|PWY0-1347|',\n", - " '|PWY-6690|',\n", - " '|PWY0-1348|',\n", - " '|PWY-5162|',\n", - " '|PWY0-1352|',\n", - " '|PWY0-1355|',\n", - " '|2PHENDEG-PWY|',\n", - " '|PWY0-1465|',\n", - " '|TRESYN-PWY|',\n", - " '|PANTO-PWY|']" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "selector\n", - "Optional Selects whether all pathways, or just small-molecule metabolism base \n", - "pathways. Can take either a symbol of :all or :small‑molecule. Defaults to \n", - ":all. \n", - "base?\n", - "Optional If this argument evaluates to true, only includes base pathways. \n", - "Otherwise, all pathways, including superpathways, will be returned. \n", - "\"\"\"\n", - "\n", - "ecoli.all_pathways(selector = 'all', base = True)[0:10]\n", - "ecoli.all_pathways(selector = 'small-molecule', base = True)[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|RXN-17635|',\n", - " '|RXN-6268|',\n", - " '|RXN-7282|',\n", - " '|RXN-10720|',\n", - " '|RXN-12870|',\n", - " '|RXN-14515|',\n", - " '|RXN-13460|',\n", - " '|RXN-14808|',\n", - " '|RXN-18819|',\n", - " '|RXN-15121|']" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "type\n", - "Optional The type of reaction to return. Defaults to :metab‑smm. The possible \n", - "values are:\n", - "\n", - ":all\n", - "All reactions. \n", - ":metab-pathways\n", - "All reactions found within metabolic pathways. Includes reactions that are \n", - "pathway holes. May include a handfull of reactions whose substrates are \n", - "macromolecules, e.g., ACP. Excludes transport reactions. \n", - ":metab-smm\n", - "All reactions of small molecule metabolism, whether or not they are present in a \n", - "pathway. Subsumes :metab‑pathways. \n", - ":metab-all\n", - "All enzyme-catalyzed reactions. Subsumes :metab‑smm. \n", - ":enzyme\n", - "All enzyme-catalyzed reactions (i.e., instances of either EC-Reactions class or \n", - "Unclassified-Reactions class). \n", - ":transport\n", - "All transport reactions. \n", - ":small-molecule\n", - "All reactions whose substrates are all small molecules, as opposed to \n", - "macromolecules. Excludes transport reactions. \n", - ":protein-small-molecule-reaction\n", - "One of the substrates of the reaction is a macromolecule, and one of the \n", - "substrates of the reaction is a small molecule. \n", - ":protein-reaction\n", - "All substrates of the reaction are proteins. \n", - ":trna-reaction\n", - "One of the substrates of the reaction is a tRNA. \n", - ":spontaneous\n", - "Spontaneous reactions. \n", - ":non-spontaneous\n", - "Non-spontaneous reactions that are likely to be enzyme catalyzed. Some reactions \n", - "will be returned for type :non‑spontaneous that will not be returned by \n", - ":enzyme. \n", - "\"\"\"\n", - "\n", - "ecoli.all_rxns(type_of_reactions = 'all')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'metab-pathways')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'metab-smm')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'metab-all')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'transport')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'small-molecule')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'protein-small-molecule-reaction')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'protein-reaction')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'trna-reaction')[0:10]\n", - "ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['|RXN-17635|']\n" - ] - }, - { - "data": { - "text/plain": [ - "['|Protein-Arginine-Aminocarbinol|',\n", - " '|PROTON|',\n", - " '|Protein-Arginine-Imidazolidine|']" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxns\n", - "A list of reaction frames. \n", - "\"\"\"\n", - "print(ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])\n", - "ecoli.all_substrates(rxns = ecoli.all_rxns(type_of_reactions = 'spontaneous')[0:1])" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|DIPYRROMETHANE|',\n", - " '|GTP|',\n", - " '|UBIQUINONE-8|',\n", - " '|AMMONIUM|',\n", - " '|LYS|',\n", - " '|HEME_O|',\n", - " '|CPD-18260|',\n", - " '|PQQ|',\n", - " '|SIROHEME|',\n", - " '|Mo-molybdopterin-cofactor|']" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.all_cofactors()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|DEOXY-RIBOSE-1P|',\n", - " '|CPD0-1546|',\n", - " '|CPD0-1545|',\n", - " '|NACL|',\n", - " '|Gramicidins|',\n", - " '|CPD0-1633|',\n", - " '|G7642-MONOMER|',\n", - " '|CPD-9229|',\n", - " '|PENICILLIN|',\n", - " '|CPD0-2358|']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.all_modulators()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|LI+|',\n", - " '|MELIBIOSE|',\n", - " '|D-GALACTURONATE|',\n", - " '|PROTON|',\n", - " '|CPD0-2241|',\n", - " '|GUANINE|',\n", - " '|Nucleosides|',\n", - " '|CPD-20888|',\n", - " '|XANTHINE|',\n", - " '|N-ACETYL-D-MANNOSAMINE-6P|']" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "from-compartment\n", - "Keyword, Optional The compartment that the chemical is coming from (see Cellular \n", - "Component Ontology). \n", - "to-compartment\n", - "Keyword, Optional The compartment that the chemical is going to (see Cellular \n", - "Component Ontology). \n", - "show-compartment\n", - "Keyword, Optional Show the form of the compound as it is present in the \n", - "specified compartment (see Cellular Component Ontology), if the compound is \n", - "modified during transport. \n", - "primary-only?\n", - "Keyword, Optional If true, filter out common transport compounds, such as \n", - "protons and Na+. \n", - "\"\"\"\n", - "\n", - "ecoli.all_transported_chemicals()[0:10]\n", - "ecoli.all_transported_chemicals(primary_only = True)[0:10]\n", - "ecoli.all_transported_chemicals(from_compartment = u'|CCO-CYTOSOL|')[0:10]\n", - "ecoli.all_transported_chemicals(to_compartment = u'|CCO-CYTOSOL|')[0:10]\n", - "ecoli.all_transported_chemicals(show_compartment = 'cell')[0:10] # not valid argument" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|CPLX0-7660|',\n", - " '|CPLX0-8247|',\n", - " '|CPLX0-3102|',\n", - " '|ACETYL-COA-CARBOXYLTRANSFER-CPLX|',\n", - " '|CPLX0-7|',\n", - " '|TRANS-CPLX-204|',\n", - " '|FLAGELLAR-MOTOR-COMPLEX|',\n", - " '|1-PFK|',\n", - " '|CPLX0-8125|',\n", - " '|CPLX0-7687|']" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "filter\n", - "Keyword The type of protein complexes to return. The argument must be one of the \n", - "following values:\n", - "\n", - ":all or t\n", - "Return all protein complexes. \n", - ":hetero\n", - "Return all heteromultimers. \n", - ":homo\n", - "Return all homomultimers. \n", - "\"\"\"\n", - "\n", - "ecoli.all_protein_complexes(filter = 'all')[0:10]\n", - "ecoli.all_protein_complexes(filter = 'hetero')[0:10]\n", - "ecoli.all_protein_complexes(filter = 'homo')[0:10]\n", - "ecoli.all_protein_complexes()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|G6165-MONOMER|',\n", - " '|PHOSPHO-NARP|',\n", - " '|G6882-MONOMER|',\n", - " '|MONOMER0-1|',\n", - " '|G7947-MONOMER|',\n", - " '|G6175-MONOMER|',\n", - " '|EG11554-MONOMER|',\n", - " '|PD01196|',\n", - " '|EG10087-MONOMER|',\n", - " '|EG10226-MONOMER|']" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "Side-Effects\n", - "\n", - "allow-modified-forms?\n", - "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", - "protein are returned. If false, then only unmodified forms of the proteins are \n", - "returned. The default value is t.\n", - "\"\"\"\n", - "\n", - "ecoli.all_transcription_factors()[0:10]\n", - "ecoli.all_transcription_factors(allow_modified_forms = True)[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|G6165-MONOMER|',\n", - " '|NARP-MONOMER|',\n", - " '|TAR-CPLX|',\n", - " '|G6882-MONOMER|',\n", - " '|EG11140-MONOMER|',\n", - " '|EG10881-MONOMER|',\n", - " '|G7947-MONOMER|',\n", - " '|G6175-MONOMER|',\n", - " '|EG12111-MONOMER|',\n", - " '|EG11554-MONOMER|']" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "class\n", - "Keyword, Optional The class |Regulation| or a subclass. It defaults to \n", - "|Regulation‑of‑Transcription‑Initiation|. \n", - "allow-modified forms?\n", - "Keyword, Optional A boolean value. If true, modified and unmodified forms of the \n", - "protein are returned. If false, then only unmodified forms of the proteins are \n", - "returned. The default value is t.\n", - "\"\"\"\n", - "\n", - "ecoli.all_genetic_regulation_proteins(class_name = u'|Regulation|', allow_modified_forms = False)[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|EG11355-MONOMER|',\n", - " '|RPOE-MONOMER|',\n", - " '|RPOD-MONOMER|',\n", - " '|RPON-MONOMER|',\n", - " '|PD00440|',\n", - " '|RPOS-MONOMER|',\n", - " '|RPOH-MONOMER|']" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.all_sigma_factors()" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[['|TU0-8814|'],\n", - " ['|TU0-8710|'],\n", - " ['|TU0-13847|'],\n", - " ['|TU0-13769|'],\n", - " ['|TU0-13667|'],\n", - " ['|TU00321|'],\n", - " ['|TU0-13385|'],\n", - " ['|TU00223|'],\n", - " ['|TU0-14243|'],\n", - " ['|TU0-14168|']]" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.all_operons()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|RXN-14142|',\n", - " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", - " '|2.7.10.1-RXN|',\n", - " '|5.99.1.2-RXN|',\n", - " '|1.5.1.34-RXN|',\n", - " '|RXN-17780|',\n", - " '|KETOACYLCOATHIOL-RXN|',\n", - " '|RXN0-7251|',\n", - " '|GLYCPDIESTER-RXN|',\n", - " '|LTAA-RXN|']" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxns\n", - "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", - "result of (all‑rxns :enzyme).\n", - "\"\"\"\n", - "\n", - "ecoli.rxns_w_isozymes(rxns = ecoli.all_rxns(':enzyme'))[0:10]\n", - "ecoli.rxns_w_isozymes()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|DCYSDESULF-RXN|',\n", - " '|RXN-14142|',\n", - " '|RXN-12402|',\n", - " '|GLUCOSE-1-PHOSPHAT-RXN|',\n", - " '|PUTTRANSAM-RXN|',\n", - " '|1.5.1.34-RXN|',\n", - " '|DHDOGALDOL-RXN|',\n", - " '|RXN-19777|',\n", - " '|RXN-12073|',\n", - " '|RXN-14285|']" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "rxns\n", - "Keyword, Optional A list of instances of the class |Reactions|. Defaults to the \n", - "result of (all‑rxns :enzyme).\n", - "\"\"\"\n", - "\n", - "ecoli.rxns_catalyzed_by_complex(rxns = ecoli.all_rxns('enzyme'))[0:10]\n", - "ecoli.rxns_catalyzed_by_complex()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|MHPELY-MONOMER|',\n", - " '|G6571-MONOMER|',\n", - " '|G7751-MONOMER|',\n", - " '|G7910-MONOMER|',\n", - " '|G6904-MONOMER|',\n", - " '|PGLUCONDEHYDRAT-MONOMER|',\n", - " '|MONOMER0-1241|',\n", - " '|ACECITLY-CPLX|',\n", - " '|G7422-MONOMER|',\n", - " '|EG12069-MONOMER|']" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\"\"\"\n", - "type\n", - "Keyword, Optional A type as taken from the argument to #'enzyme?. Defaults to \n", - ":chemical‑change.\n", - "\n", - ">> type\n", - "Optional Can take on one of the following values to select more precisely what \n", - "is meant by an “enzyme”:\n", - "\n", - ":any\n", - "Any protein that catalyzes a reaction is considered an enzyme. \n", - ":chemical-change\n", - "If the reactants and products of the catalyzed reactin differ, and not just by \n", - "their cellular location, then the protein is considered an enzyme. \n", - ":small-molecule\n", - "If the reactants of the catalyzed reaction differ and are small molecules, then \n", - "the protein is considered an enzyme. \n", - ":transport\n", - "If the protein catalyzes a transport reaction. \n", - ":non-transport\n", - "If the protein only catalyzes non-transport reactions. \n", - "\"\"\"\n", - "\n", - "ecoli.all_enzymes()[0:10]\n", - "ecoli.all_enzymes(type_of_reactions = ':any')[0:10]\n", - "ecoli.all_enzymes(type_of_reactions = ':chemical-change')[0:10]\n", - "ecoli.all_enzymes(type_of_reactions = ':small-molecule')[0:10]\n", - "ecoli.all_enzymes(type_of_reactions = ':transport')[0:10]\n", - "ecoli.all_enzymes(type_of_reactions = ':non-transport')[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['|DCUA-MONOMER|',\n", - " '|G7399-MONOMER|',\n", - " '|YIDT-MONOMER|',\n", - " '|CORA-MONOMER|',\n", - " '|EG12134-MONOMER|',\n", - " '|EG11486-MONOMER|',\n", - " '|CYNX-MONOMER|',\n", - " '|YJDL-MONOMER|',\n", - " '|EG11512-MONOMER|',\n", - " '|GLTP-MONOMER|']" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ecoli.all_transporters()[0:10]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/setup.py b/setup.py index ea61da8..6e698f7 100644 --- a/setup.py +++ b/setup.py @@ -22,19 +22,19 @@ # Always prefer setuptools over distutils from setuptools import setup, find_packages +# To use a consistent encoding from codecs import open -from os import path -# include example folder -import glob +from os import path, walk def main(): - # add examples folders + # additional files data_files = [] - directories = glob.glob('example/*/*/*') - for directory in directories: - files = glob.glob(directory+'*') - data_files.append((directory, files)) - print(data_files) + for dirpath, dirnames, filenames in walk('examples'): + tmp = [] + for filename in filenames: + tmp.append(path.join(dirpath, filename)) + data_files.append((dirpath, tmp)) + #print(data_files) # Get the long description from the README file here = path.abspath(path.dirname(__file__)) @@ -44,20 +44,28 @@ def main(): setup( name='PythonCyc', license='SRI International', - version='2.0', + version='2.0.1', description='A Python interface to Pathway Tools, 2019 update', long_description=long_description, #long_description_content_type='text/markdown', url='https://github.com/networkbiolab/PythonCyc', author='Rodrigo Santibáñez', author_email='glucksfall@users.noreply.github.com', + + python_requires='~=3.0', keywords=[], - packages=find_packages(exclude=['contrib', 'docs', 'tests']), install_requires=[], - package_data={ - 'example' : ['example'], - }, + + # include files + # MANIFEST.in, sdist + include_package_data=True, + # bdist_wheel (only for non-python files inside of the package) + packages=find_packages(exclude=['contrib', 'docs', 'tests']), + #package_data = { + #'PythonCyc' : ['test/*.txt'] + #}, data_files=data_files, + project_urls={ 'Manual': 'https://pythoncyc-v20.readthedocs.io', 'Bug Reports': 'https://github.com/networkbiolab/PythonCyc/issues', From 99cae199ca7d66dc8deb336a512e603ffb876150 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Santib=C3=A1=C3=B1ez?= Date: Fri, 10 Jan 2020 14:53:16 -0300 Subject: [PATCH 13/17] updated setup.py to include examples in sdist and wheel --- MANIFEST.in | 1 + 1 file changed, 1 insertion(+) create mode 100644 MANIFEST.in diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..6311329 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1 @@ +include examples/*ipynb From ec6f4f4c8914e12a16f449564bb051987bcab1b0 Mon Sep 17 00:00:00 2001 From: Rodrigo Date: Tue, 7 Jul 2020 18:25:20 -0400 Subject: [PATCH 14/17] typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c71baa4..56f887b 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ Overview An updated version of the original PythonCyc API from Mario Latendresse. -This module has been testes under Python 3.6 and Python 3.8, with examples +This module has been tested under Python 3.6 and Python 3.8, with examples at https://github.com/networkbiolab/PythonCyc/tree/master/examples Disclaimer: a number of functions remains broken. From e761e2c9874f00763109c04475db796a5cde152a Mon Sep 17 00:00:00 2001 From: Rodrigo Date: Tue, 7 Jul 2020 18:30:49 -0400 Subject: [PATCH 15/17] Makefile --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6e698f7..84a3f3c 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ def main(): setup( name='PythonCyc', license='SRI International', - version='2.0.1', + version='2.0.2', description='A Python interface to Pathway Tools, 2019 update', long_description=long_description, #long_description_content_type='text/markdown', From 177f32701d81566c7c440e3ca1a9062b6f374ec1 Mon Sep 17 00:00:00 2001 From: Rodrigo Date: Tue, 7 Jul 2020 18:38:41 -0400 Subject: [PATCH 16/17] Makefile --- Makefile | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 Makefile diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..d04765b --- /dev/null +++ b/Makefile @@ -0,0 +1,11 @@ +build-package: + rm -rf build + rm -rf pleione.egg-info + rm -rf __pycache__ + python3 setup.py bdist_wheel sdist + +clean-package: + python3 setup.py clean + +install-package: + python3 setup.py clean build install From 9788f14916a3d4fef3bfeb1088d040dc9054063d Mon Sep 17 00:00:00 2001 From: Rodrigo Date: Tue, 7 Jul 2020 21:13:26 -0400 Subject: [PATCH 17/17] Makefile --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index d04765b..f34f1c2 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ build-package: rm -rf build - rm -rf pleione.egg-info + rm -rf PythonCyc.egg-info rm -rf __pycache__ python3 setup.py bdist_wheel sdist