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.
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