How to use get_mol() on pdb proteins?

[dschlesinger]

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.

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

Any updates on this?

[ptosco]

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

[dschlesinger]

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,