Use sdf/molfile instead of pdb

[VittorioRainaldi]

Hi,

is it possible to do diffusion using a small molecule ligand that is not part of a pdb?
For example an sdf file downloaded directly from pubchem or even generated in a molecular editor software such as avogadro.
I tried converting sdf into pdb but I get an error when the parse_pdb function does not find a sequence in the input pdb.

idx_sm = torch.arange(max(idx_prot),max(idx_prot)+Ls[1])+200
ValueError: max() arg is an empty sequence

As far as I understand the diffusion process is not using the protein sequence at all, so it should be possible to take an isolated ligand as input but I couldn't find a way to do it.

As a side note it would be nice to have some more comments in this code, otherwise it's really hard to figure out what's what.

Best,
Vittorio

[samholtzen]

I'm currently having a similar issue. Has anyone solved this?

[VittorioRainaldi]

Hi, I was able to run the code with a simple but ugly hack which is taking my ligand and adding it into a random pdb of an enzyme without a ligand. I didn't delve super deep into the code but from what I can tell it's set up to simply discard anything that is not the ligand anyway.