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SeonghwanSeo / PharmacoNet

Official Github for "PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling" (NeurIPS 2023 Workshop)
https://arxiv.org/abs/2310.00681
MIT License
44 stars 4 forks source link

a small problem with quotations #2

Closed yordan-ov closed 2 months ago

yordan-ov commented 7 months ago

First i want to congratulate you on the great tool.

I noticed a small error with quotations when trying to run the provided examples. It runs fine if i don't put the input chemical in quotations. Provided the details below:

E:\programs\PharmacoNet>python scoring.py -p ./examples/6OIM_model.json -s 'c1ccccc1' --num_conformers 8

*** Open Babel Error in OpenBabel::OBSmilesParser::ParseSimple SMILES string contains a character ''' which is invalid Traceback (most recent call last): File "E:\programs\PharmacoNet\scoring.py", line 43, in score = scoring(args.smiles, model, args.num_conformers) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "E:\programs\PharmacoNet\scoring.py", line 21, in scoring pbmol = pybel.readstring('smi', smiles) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "xxx\Programs\conda\envs\pmnet\Lib\openbabel\pybel.py", line 209, in readstring raise IOError("Failed to convert '%s' to format '%s'" % ( OSError: Failed to convert ''c1ccccc1'' to format 'smi'

SeonghwanSeo commented 7 months ago

Hello @yordan-ov, Thanks for letting me know. I am currently only running it on LINUX and MAC environments and have not checked its behavior on WINDOW environments, so I am not aware of this issue. I will add documents on different OS environments in the future.