2021-10-13 Pulido/Wagner Meeting notes

General updates

• JW –

  • Talked with PIs including John, we’ve agreed that TypedMolecule is not a top priority for the initial set of biopolymer support features.

  • Merged TopologyMolecule-removing PR

  • Next I’ll work on either “playing nice with the OpenMM topology hierarchy” or general bugfixing and usability

• JW – On Friday, I’ll start working on from_pdb, doing the leaving-atom-permutation-dance, and figuring out how to do peptide bond order assignment (because there aren’t substructures that overlap with both sides of the peptide bond)

• IP – I’ll commit the code that I have now, and continue doing cleanups and adding tests. Add tests with the things that are failing now