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rdkit / rdkit-js

A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .
https://rdkitjs.com
BSD 3-Clause "New" or "Revised" License
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How to use get_mol() on pdb proteins? #416

Open dschlesinger opened 8 months ago

dschlesinger commented 8 months ago

I noticed you can't use the get_mol() function on pdb files, I was trying to use morgan fingerprint encoding on protein and ligand for an ML application. Wondering if that is possible using RDKIT-JS. Is there a similar functionality to getMolFromPDBFile().

It works on smiles but returns null when given a PDB format. I also noticed that you can use a JSON for get mol. What format would that take and could I use that for my protein? Documentation was unclear.

ghost commented 8 months ago

I had the same problem, but I could not find a solution. Can anyone help?

ghost commented 7 months ago

Any updates on this?

ptosco commented 7 months ago

get_mol currently takes SMILES, CXSMILES and CTAB strings as input, not PDB strings.

dschlesinger commented 7 months ago

Hi, thank you for your response!

Do you know of any way to load a pdb file in js? Am probably going to switch to Python to utilize that version of rdkit. However it would be optimal to use js.

Thanks,