Issues setting the conda environment

[dfreire1]

Hello,

I've been trying to get LUNA up and running, but the specific .yml file for the environment has been either taking long time in setting up to the point that it doesn't continue or finishes with errors. Is there any update or advice regarding how to set up the environment?

I also tried manually installing the packages, but I've been running into incompatibilities. So I was wondering if there's any updates.

Thank you!

[alexandrefassio]

Hi David,

This issue was caused by an outdated version of Biopython. I've already resolved the dependency and code issues that were preventing support for the latest Biopython releases. I'm now in the process of running additional debugging and testing.

ASAP, I'll update LUNA.

Until the final version is available, one thing you can try is to update the biopython and the Python versions in the YML.

Let me know if that helps.

[dfreire1]

Hi Alexandre,

Thank you so much for your quick response. I'm going to solve the environment using python=3.9 and no version pinned for biopython and see how it goes

[dfreire1]

Alexandre,

I changed the .yml file and I was able to solved the environment.

name: luna-env
channels:

• anaconda
• schrodinger
• conda-forge
• defaults
  dependencies:
• python=3.9
• rdkit
• seaborn
• openbabel
• pip
• biopython
• pymol
• xopen
• colorlog
• networkx
• scipy
• pip:
  • mmh3==2.5.1
  • pdbecif

Nevertheless, I can't install luna through pip. I get the error I'm leaving below. You mentioned that you need to update luna, but I'm not sure if you referred to the repo or the package luna through pip

pip install luna
Collecting luna
Using cached luna-0.13.1.tar.gz (1.4 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [22 lines of output]
/project/pharmacology/FLiu_lab/shared/miniforge3/envs/luna-env/lib/python3.9/site-packages/openbabel/init.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel"
warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')
/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/MyBio/PDB/PDBParser.py:473: SyntaxWarning: "is" with a literal. Did you mean "=="?
if (serial_number is ''):
Traceback (most recent call last):
File "", line 2, in
File "", line 35, in
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/setup.py", line 28, in
from luna.version import version
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/init.py", line 2, in
from luna.projects import Project, LocalProject
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/projects.py", line 16, in
from luna.config.params import ProjectParams
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/config/params.py", line 7, in
from luna.mol.entry import *
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/mol/entry.py", line 25, in
from luna.MyBio.PDB.PDBParser import PDBParser, WATER_NAMES, DEFAULT_CHAIN_ID
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/MyBio/PDB/init.py", line 17, in
from .MMCIFParser import MMCIFParser
File "/tmp/pip-install-56xtay2k/luna_27390115744041a8a4b78c0784105635/luna/MyBio/PDB/MMCIFParser.py", line 27, in
from Bio._py3k import range
ModuleNotFoundError: No module named 'Bio._py3k'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[dfreire1]

Hi Alexandre,

I was also thinking, do you have this repo currently running in a machine? I was wondering if it would be easier to make a dockerfile that I can easily transfer over.

I appreciate you looking on this, thank you!

[alexandrefassio]

Hi @dfreire1,

Sorry for taking so long to get back to you. I have just updated LUNA to 0.14.0. In this version, I removed the dependency on the legacy Biopython.

Try to install LUNA again using pip and the new env file. Let me know if it works for you now.

bests

[dfreire1]

This is great news! Thank you so much for your support. I'll test it out.

[knk9596]

Hi Alexandre,

I used the following yml file to set up conda enviroment:
name: luna-env
channels:

• conda-forge
• schrodinger
• defaults
  dependencies:
• python
• rdkit
• seaborn
• openbabel
• pip
• biopython>=1.77
• pymol
• xopen
• colorlog
• networkx
• scipy
• pip:
  • mmh3>=2.5.1
  • pdbecif

But I got the errors as follows:
/sc/arion/work/zhaoy14/test-env/envs/luna-env/lib/python3.12/site-packages/openbabel/init.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel"
warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')
Module 'simplejson' not available. Built-in module 'json' will be imported.
Module 'simplejson' not available. Built-in module 'json' will be imported.
Traceback (most recent call last):
File "/sc/arion/projects/zhangb03a/zhaoy14/LUNA/luna/run.py", line 8, in
from luna.interaction.view import InteractionViewer
File "/sc/arion/work/zhaoy14/test-env/envs/luna-env/lib/python3.12/site-packages/luna/interaction/view.py", line 3, in
from luna.wrappers.pymol import (PymolWrapper, PymolSessionManager,
File "/sc/arion/work/zhaoy14/test-env/envs/luna-env/lib/python3.12/site-packages/luna/wrappers/pymol.py", line 11, in
from Bio.Data.SCOPData import protein_letters_3to1
ModuleNotFoundError: No module named 'Bio.Data.SCOPData'

I am wondering if it has anything to do with the biopython version? For now I am using 1.86.

Any advice would be greatly appreciated! Thank you so much!

Yihan