Molecules in getVoxelDescriptors() about moleculekit HOT 5 CLOSED

Do you have concrete cases that SmallMol does not work? Could you post them here? In the paper we used autodock to get the features but we have dropped this since then to be more independent and have better control. We have been able to reproduce it afaik with SmallMol.

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Also no, don't disable the validity checks. You will just get garbage out if you pass a small molecule with as a Molecule object in.

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Well the problem with the SmallMol is mentioned in Issue #12. There is also a file as example. In general, from the ca 3700 Complexes of the refined dataset of pdbbind, around 1200 ligands can not be readed in as SmallMol.
The reason is in rdkit. So at the problematic ligands, it is not possible to create a molecule-object in rdkit and because of this, it is not possible to create a SmallMol with moleculekit or HTMD.

The support of accelera, said that I can use Molecule instead of SmallMolecule. But like you mentioned, I would need to disable the validitychecks.

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Ok, let's continue in the other issue then for now

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@BioFreak95 I will close this issue as you should not use Molecule for small molecules in getVoxelDescriptors. Check #12 to see my analysis of the issue with the problematic molecule.

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