HISTORY.txt

0.764: 1 July 2008: GWV
    - Rewrote RMSD calculation routine (much, much quicker); now part of molecule class (moved RmsdResult, Ensemble, Model, etc
      classes as well).
    - Ranges used for superpose are stored as molecule attribute and used for rmsd calculations on restoring the molecule instance.
    - Fixed bug using script option on command line.
    - changed numpy.arange import in NTplot to Numeric.
    - worked on the refine routines.
    - Improved the Makefile
    - main: --shiftx, --superpose options

0.76: 23 Jun 2008: GWV
    - project.molecules is now a _ProjectList instance (used to be a NTlist instance with names)
      molecule names are stored now in moleculeNames attribute
      preferentially used the names() method of molecules, peaks, distances and rdcs to get the names of the list
      to loop over all molecule instances:
        for mol in project.molecules:
    - All project objects (like a Molecule or PeakList) have an attribute 'objectPath' which contains the full CING path and is used as default
      for saving;
      i.e. myMolecule.save() should work
    - project.version is a float (used for version comparison)
    - new project.reports: NTlist instance: to hold the validation report names (not yet implemented, but who knows!?)
    - Defined a 7-element name tuple:

        (moleculeName, chainName, resNum, atomName, modelIndex, resonanceIndex, convention)

      Allows referencing of an object at the Project level:

      hence

      Project.decodeNameTuple( nameTuple ); also works from the Molecule level: Molecule.DecodeNameTuple( nameTuple )

      Implemented for Molecule, Chain, Residue, Chain, Atom, Resonance, Coordinate
      TODO: Peak, PeakList, etc...

      The 4-element nameTuple still works from the Molecule level!

    - Hash in molecule.nameTuple
    - SML >=0.2: recursion implemented.
    - New Molecule storage in one file using SML routines; conversion routines implemented.
    - PeakList storage updated using SML >0.2. Employs the 7-element nameTuple format.
    - Peak class updated: now has NTvalue for height and error; likewise for volume; hasHeight() and hasVolume() methods
    - Resonances have NaN as undefined, rather then NOSHIFT.
    - Molecule.resonanceSources: a simple list to store the source from which the resonances were derived; e.g. all-final.prot
    - All SML routines in file sml.py; prevent circular imports; one import in cing.__init__ (this file) needed to activate.
    - NTaverage returns NaN for n=0, n=1.
    - NTvalue uses NaN as initiating (value, error)
    - Improved output using NTdetail.

Version 0.751: 1 May 2008:
    - Added superposing algorithm mostly in cython.
    - Added chi1/2 plots labeled Janin plots

Version 0.75: 17 Apr 2008:
    - Optimized the coordinate storage class for speed through cython now.
    - Temp dir now set in $CINGROOT/python/localConstants.py or __init__.py by default.

Version 0.74: 25 Mar 2008:
    - Optimized the coordinate storage class for speed.
    - Added water to topology.
    - Added user settings in a standard localConstants.py
    - Improved processing of X-ray structures as done by getPhiPsi.py script
    - Added trivial parallelization of running over multiple molecules.

Version 0.73:  3 Mar 2008:
    - Started to look into incorporating Queen. Need Swig update.
    - Created test code for drawing residue plots with secondary structure
        icons above it ala Procheck_NMR.

Version 0.72: 12 Jan 2008:
    - Added extensive test cases. Call all by cing --test.
	- Added integration with Aqua, Molmol, Povray, convert and ps2pdf
	- Started migration to matlibplot away from biggles. Needs more testing.

Version 0.71: 05 Dec 2007:
    - reformatted the version/copyright formatting
    - redid the determination of the CINGROOT and checks in setup.py
    - added --test option to main.py but needs beautification;-)
    - renamed NTstruct to NTdict (including in the dbTable)
    - exercised the feature request system in sf.net.
    - Changed DOS eol in cing/__init__.py to Unix.

Version 0.70: 03 Dec 2007:
    - Reorganized for easy integration with Eclipse/PyDev
    - Removed wild imports to accommodate the imports as PyDev suggests.
    - Organized import statements by PyDev.
    - Replaced many variable names to dummy if their values aren't used anymore after assignment.
        This is then no longer flagged by PyDev as a potential bug.
    - Moved version.py to __init__.py
    - Renamed main script from cing.py to main.py to prevent possible name space clashes.
    - Removed cing.par for now.
    - Removed development.py
    - Moved history from __init__.py to here.
    - Removed simple brackets as in: "if (verbose):"
    - Added What If to setup.py and reorganized.
    - Moved main development to sourceforge.net
    - Reorganized python code so that all falls under Python cing package with
        just one path to be added to PYTHONPATH namely CINGROOT/python.
    - Introduced some java library code for working with Wattos.
    - Removed shiftx.osx binary as it was not used in on JFD's Mac OS X machine.
    - Introduced some test data for entry 1brv; see cing.PluginCode.test.test_all.py
    - Failed to get cing.PluginCode.validate.py working completely.
    - Failed to get cing.PluginCode.ccpn.py working as it references the old ccpn
        api (branch 4?).

Version 0.520: 16 Oct 2007: Merged version GV and Alan
    classes.py:
         - <a class="red"...</a> solution
         - new method insertHtmlLinkInTag()
    cing.css:
         - new entries for #main class
    ccpn.py:
         - fix bug about atoms when importing distance restraints
         - removed old Ccpn stuff
    validate.py:
         - using pseudo atoms for shift average in validateAssignments()
         - moved findHtmlLocation() to classes.py
         - fixed html output code according W3C
         - started to modify Residues html pages
    cing.py:
         - removed old Ccpn stuff

Version 0.513: 16 October 2007:
- included IPython library
- Fixed a serious bug in export routine to toPDB from atom properties that caused the first model to be skipped in lieu off
  the last model.

Version 0.512: 15 October 2007:
- Completed the procheck ranges option and import of results routines.

Version 0.51: 10 October 2007
- classes.py:
    - new SML storage approach (import SMLhandler)
    - new RDCRestraint and RDCRestraintList classes implemented (to be tested)
    - class ProjectList has 2 new methods save/restore, 2 new initialising
      arguments and fixed appdend()
    - Project.export() has a new verbose approach
    - move class Peak from molecule.py to classes.py
    - all ProjectList (eg. Peaks, Distances etc.) classes has a SMLhandler
    - removed residue and angle attributes (no longer mandatories)
    - new retrieveDefinition method to return a known dihedral angle
    - new calculateAverage method for class DihedralRestraint
- molecule.py:
    - speed up of restore of Molecule as well as less memory usage
    - new attribute dihedralDict for Molecule
- pdb.py:
    - skip cyana pseudo residues
- validate.py:
    - new text output approach (method mprintf)
    - generating Html for Restraints, Peaks and main project.
- NTutils.py:
    - new methods minItem, maxItem for class NTlist
    - class NTvalue inherit from NTdict now (not NTstruct anymore) and has more
      arithmetic operators (==, !=, >, >=, <, <=)
    - fixed some calls Value to NTvalue in class NTvalue
    - new function list2asci
- cyana2cing.py:
    - parser.add_option has "export"
- sml.py:
    - new file with class SMLhandler
- xplor.py:
    - delta adjusted to delta*0.5
- cing.py:
    - little change in function formatall()
- TODO:
    - implement importFromCcpnRdcRestraints() in ccpn.py
    - remove initCCPN (old implementation) from cing.py
    - define a testing code way.

Version 0.50: 20 September 2007
- New structure for directories

Version 0.48: 23 August 2007
- Version for overhaul validation
- classes.py:
    - peakLists is gone. Now it's 'peaks'
    - new method to class Project: self.mkdir(dir)
    - new paramenter 'restore': if False, only project description is loaded
    - newPeakList, appendPeakList are obsolete
    - verbose in ProjectList.new()
    - new method to class ProjectList: self.toFile(), for internal storage
    - new parameters (in __init__) and methods for class DistanceRestraints:
      calculateAverage, listViolatingModels, _names
    - new parameters (in __init__) and methods for class DistanceRestraintList:
      append, analyze, sort
    - new htmlObjects (NTlist)
    - new method 'path" (returns where Cing is installed): better change this
      name!!!
- validade.py:
    - new setupValidation (validateDistanceRestraints)
    - validateAssignments expanded
    - new findHtmlLocation()
    - new setupHtml
    - new renderHtml
- NTutils.py:
    - class NTlist has new methods: min, max, sumsq, sum, limit
- parameters.py:
    - new project directory structure
    - new dict htmlDirectories
- molecule.py:
    - updateDihedrals is now updateAll
    - new methods residuesWithProperties, atomsWithProperties in classes
      Molecule, Chain, Residue and atomsWithProperties in Atom; hasProperties in
      classes Atom and Residue
    - new behaviour for method distance in class Atom
    - new method meanCoordinates and realAtom in class Atom

Version 0.47: 12 June 2007
- improved setup.py to enable CING for bash users
- CCPN import/export by Alan
- Many more things

Version 0.46: 23 May 2007
- Fixed serious bug Molecule.decodeNameTuple which generated errors of CYANA
  Lys+/ARG+ import/conversion.
- --validate option in cing.py
- Update of dbTable
- Changed Analysis directory to Validation/Cing

Version 0.45
- Fixed refinement stuff, related to PSF generation
- Smaller bugs

Version 0.44
- implemented isProton, isCarbon, isNitrogen methods of Atom class.
- peakList or peak attribute xeasyColor
- exporting peaksList with xeasyIndices in steps of 10000
- exporting prot file with xeasyIndices [1,n] for each molecule
- Fixed database topology error MET QE
- Changed database PHE/TYR QR real definition, removed pseudo for QD/QE
  now is more like the VAL QQG or LEU QQD defs.
- Cosmetic stuff on the output

version 0.43
- Wim Franken's integration with CCPN stuff.

Version 0.42
- Implemented importUpl, importAco methods of Project class
- Integrated refine stuff
- New setup for PYTHONPATH and the like: setup.py script generates
  cing.csh script.
"""