Input direct from PDB file fails

[alexhilditch]

Hi there,

Thanks for the early release of the model, it's great to look at and play around with!

I am having issues with running predictions with ligands directly from a PDB file. It appears to be an issue with finding chiral centres with rdkit. Both the examples modelforge/tests/data/example_from_pdb_with_inter_chain_bond.pdb and modelforge/tests/data/example_pdb_with_clashing_ligand_name.pdb fail when loaded directly with rf3 fold inputs='modelforge/tests/data/example_from_pdb_with_inter_chain_bond.pdb'

Symptoms: the prediction hangs for a long time at WARNING:atomworks.ml.transforms.rdkit_utils:Initial conformer generation based on distance geometry failed. Successful: 0. Falling back to generating a conformer starting from random coordinates. example_pdb_with_clashing_ligand_name hangs for approx 2 hours. example_pdb_with_inter_chain_bond hangs for over 12 hours.

Afterwards it fails to find chiral centres with rdkit, and the run fails.

PDB files with no ligand run successfully. Log files attached for both examples.

Thanks.

example_pdb_with_inter_chain_bond.log example_pdb_with_clashing_ligand_name.log

[nscorley]

Thank you for raising this issue! We're aware and looking into it; we'll have a patch soon