JW – Great work on Interchange docs - MT is super pleased.
JW – DNolasco starting moving on “how to cite” on main website - Maybe we could convert this to “open PR to add some sort of automation that creates bibtex blocks from publications.yaml”?
JM – I could do that, but I’m mostly busy with interchange for the near future.
JM – Will reading multicomponent PDBs be supported in biopolymer toolkit?
JW – Not in the current functionality, but I’ve been thinking about this:
Recognizing small molecules vs. polymers
Right now we have Molecule.from_pdb_and_smiles and Topology.from_openmm (which can basically read PDB but needs unqiue mols) and we will be adding Molecule.from_pdb. The former is for use with PDBs containing small molecules, and the latter is only for proteins. So in reading a mixed pdb, the chemical-recognition logic would need to figure out what’s a small molecule vs. a protein.
JM – I think we could really improve things by adding a Topology.from_pdb_and_smiles
JW – That’s a good idea. It may be cleaner to have like Topology.from_pdb_and_unique_molecules (or something that works this way but has a less teirrble name)
JM – Molecule.from_polymer_pdb may be a better name for what we’ll be adding
JW – Good idea, I’ll change that
Missing atoms (eg loops)/how much to trust mutually-connected subgraphs?
(medium) Toolkit revised user guide (+-unifying/centralizing package user guides)
(medium) Come up with “milestones” for making first of three videos this year (like, “first video on covid spike protein and small molecule, filmed this day, edited in that range, etc…”)