Handle edge case in `utils.py`

chemosim-lab / ProLIF

Interaction Fingerprints for protein-ligand complexes and more

https://prolif.readthedocs.io

Apache License 2.0

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Handle edge case in `utils.py` #205

Closed amorehead closed 1 month ago

amorehead commented 1 month ago

Handles an edge case in utils.py that would normally lead to an RDKit-caused segmentation fault upon calling SplitMolByPDBResidues(mol) on certain molecule (single-fragment) inputs.

exs-cbouy commented 1 month ago

Hi @amorehead and thanks for opening a PR, it's really appreciated 🙌

Regarding the issue, I've only encountered the segmentation fault when the input mol was missing residue information for SplitMolByPDBResidues to function correctly. There's already the prolif.Molecule.from_rdkit method to wrap around this problem by adding dummy residue info, is that enough to fix your problem?

amorehead commented 1 month ago

Hi, @exs-cbouy. Thanks for pointing out that this issue can be avoided by using prolif.Molecule.from_rdkit! In which case, I think we can close this issue, as that resolves the root concern on my end.