2022-02-23 Mitchell/Wagner Check-in meeting notes

Participants

  • @Jeffrey Wagner

  • @Josh Mitchell

Discussion topics

Item

Notes

Item

Notes

Updates

  • JW – Updates on Bespokefit

  • JW – Biopolymer release testing+migration guide+example (“Unofficial” PTM functionality?). Not ready yet, I’ll let you know when the alpha is cut.

    • JW – There may be an existing notebook with the “aspirational API” that could be used as a starting point

    • JM – I’ll only get to use this for the first time once, so I might plan to start without material so that I can get a good “Test run” in first and understand what needs to be documented/communicated better.

    • JM – Should we deprecate/replace the toolkit showcase after the biopolymer release?

      • JW – I think we should make a new example, even if it covers the same ground, since I still want to show people how to use the old pathway (even if we label it as “no longer recommended”)

      • JM – Agree, the old example will help cover cases where people NEED to import eg. ligand parameters from other parameterization engines.

  • JW – The two things I may contact you for outside this meeting are

    • “The toolkit alpha is ready, please start trying to break it”

    • “Bespokefit is ready, please start working with bill swope on it”

Todos

  1. Feb 23 TODO FOR JEFF: Follow up on COOH conformer PR (approve if no feedback)

  2. (high) QCSubmit users guide (in progress)

  3. (high) ELF10 COOH conformer rotation issue (MERGED!)

  4. (medium) Toolkit API desire paths (MERGED!)

  5. (medium) Toolkit docs cleanup

  6. (medium) Toolkit revised user guide

  7. (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…”)

  8. (low) “How to cite” section on website (do not start, pending feedback)

  9. (low) Check main website for broken links

  10. (low) migrate docs to be under http://openforcefield.org

  11. domain (openforcefield/status would be base project repo)

  12. (low) Conda env yamls for each release (automated inside of Toolkit’s single-file-installer action)

Trello bookkeeping

(Added “work on videos”, packmol breadcrumb )

Action items

Decisions