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sc8668 / RTMScore

MIT License
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Some of the ligands in CASF core set cannot be read by RDKit successfully #6

Closed omotcha closed 1 year ago

omotcha commented 1 year ago

Hi Chao Shen, thanks for your work! I tried to evaluate RTMScore on CASF benchmark and it turned out that some of the ligands in CASF core set cannot be read by RDKit successfully thus the proceeding steps could not be done. If I added sanitize=False to Chem.MolFromMol2Block and Chem.MolFromMolBlock in RTMScore/RTMScore/data/data.py line 149 and 153, RDKit could read those ligands but I noticed that this would cause a slight difference to the final prediction. So I wonder if you ever encountered and how you handle this problem. Thanks.

sc8668 commented 1 year ago

Some ligands in CASF benchmark have some mistakes, so in our study we re-converted all the ligands to SDF format with the convert.py script implemented in OpenEye software, and this could make almost all the ligands recognized by RDKit.

omotcha commented 1 year ago

Thanks!