2024-07-29 Mitchell/WagnerCheck-in meeting notes

General updates

• JW –

  • I’m re-recording my demo since sound was off at OMSF symposium

    • JM – Recommend using OBS for recording/sound splicing.

  • Reminder to clockify for July at the end of this week

  • FYI - Excientia is using the MDAnalysis guesser and is pretty happy - https://github.com/openforcefield/openff-toolkit/issues/1828#issuecomment-2251643771

• JM –

  • Updates on PDBFixer - Updated it so the residue template reader records formal charge and bond order. But there’s only room in the Topology object for bond orders, and the CCD has options for SING, DOUB, TRIP, QUAD, AROM, DELO, PI, and POLY, the latter of which aren’t too useful for us. I think knowing formal charges could be enough to derive them chemical info though.

  • JW – Ok, a few thoughts:

    • This looks good. Feel free to open a PR when you’re ready

      • JM – I recall there was a bug, looking into it now.

    • Not sure if this gets us all the way to unambiguous

      • JM – We should be able to use formal charge to guess and check with the MDA guesser

      • JW – Good point

    • PE pointed out that my approach, we don’t avoid “guessing” with general chemical rules, instead we just use general rules to enumerate protonation variants.

  • …

  • JM – Any comments on the changes I’ve made in this branch?

    • JW – Nope, that looks great.

Trello

https://trello.com/b/dzvFZnv4/infrastructure