2021-06-11 Biopolymer Topology Meeting notes

Working session

• Can we make a to-do list of remaining edge cases for the perception functionality?

  • (made remaining to-do list in PR #973, will merge remaining items into body text of #951)

• IP – Alanine is coming up as non-isomorphic when loaded from PDB vs. SDF

  • (SOLVED – We worked on this, it was because atom_stereochemistry_matching wasn’t being ignored)

• There’s some trouble with mainchain proline

  • This is because one of the substructures from aa_variants is getting a negative charge on the nitrogen. We’re not sure why. Added as a to-do item in the PR.

PRs

• Residue perception

  • Conflicts resolved + merged

• Substructure database maker

  • Merged

Ensuring top-level page has links to current resources

• Where should the adding-bond-orders-to-PDB progress go?

  • We’ll put it on IP’s toolkit branch
    
    

Possible interest in continuing after move to NY if John approves?

• JW – Would this be of interest?

  • IP – Yes, maybe not all the way to the end, but there are some things I’d like to finsih up

  • JW – I’ll start a conversation with JC about this