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HannesStark / EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
MIT License
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Can't kekulize mol. Unkekulized atoms #31

Closed Harry4FunResearch closed 2 years ago

Harry4FunResearch commented 2 years ago

I got a lot of the following errors. Any idea what went wrong? Thanks.

[15:06:44] Can't kekulize mol. Unkekulized atoms: 14 15 16 17 18 [15:06:44] Can't kekulize mol. Unkekulized atoms: 8 9 10 11 12 13 14 15 16 [15:06:44] Can't kekulize mol. Unkekulized atoms: 40 41 42 43 44 ....

update: Reinstall of psutil fixed the problem.

HannesStark commented 2 years ago

That sounds to me like RDKit cannot sanitize your input molecules. Probably you will have more success in finding what causes these errors for your ligands when just googling the error. I do not know what causes RDKit to throw them

yufengwhy commented 2 years ago

I met the same problem, and install psutil, but the problem remains, any advices? @HannesStark