How to use get_mol() on pdb proteins?

Question

How to use get_mol() on pdb proteins?

dschlesinger opened this issue a year ago · 4 comments

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.

Answer 1 · 2023-11-04T19:23:57.000Z

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

Answer 2 · 2023-11-15T02:02:09.000Z

Any updates on this?

Answer 3 · 2023-11-15T10:07:34.000Z

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

Answer 4 · 2023-11-16T00:46:59.000Z

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,