2021-12-20 Core Developers meeting notes

General updates

• No core-devs next week.

Individual updates

• JW –

  • Worked on biopolymer cleanup (refactoring Molecule.from_pdb code to use wither ToolkitWrapper and for logic to be in appropriate places). Also thinking about good architecture for whole workflow - Ultimately we want something like Topology.from_pdb, but this will require some dancing around with openMM to load hierarchy info and recognize residues from PDB info and add CONECTs, then networkX to identify individual mols and add chemical info. So Topology.from_pdb will need to identify each component in the input and figure out whether it’s a small molecule from the unique_molecules kwarg, or whether it is a polymer and should to have chemical info assigned by a substructure library. And Molecule.from_pdb will need to detect whether the input is really more than one molecule and raise an error if so.