2023-03-29 Mitchell/Wagner Check-in meeting notes

General updates

• JW — Did you meet MForster at tea time?

  • JM – Yeah, cool guy. He’s in favor of centralized docs.

• JW – I’m working on multicomponent PDB loading. Can load 75k atoms (protein+ligand+water+ions) in 15 sec. Does that sound good?

  • JM – That could be better but it’s not terrible. Consider multicore in the future?

  • (JW shows proposed API)

  • JW – I’ll aim to get this in a release ASAP

  • JM – Would this be faster if combined with pdbinf?

  • JW – Yes, I think that could be a good final product, once both are production-ready.

• JW — MT will be running an Interchange workshop in the UK in September, may ask you for assistance in preparing material/reusing as docs.

• JW – We’re trying to figure out how to measure outreach and community engagement

  • JM – I think ecosystem docs would be really good - A lot of people said that it’s hard to figure out which packages are available/which to use for their tasks.

• JM – I’m gonna try to cut a bespokefit release in the next week. Never done one before

  • JW – I’m happy to screenshare for it, could loop in MT as well if the timing works. Just let me know once you’re ready to go and we’ll schedule a session.

Trello update

To dos

1. (high) Getting bespoke tests green

2. (medium) BespokeFit 0.2.1 (or some sort of release that works with OFFTK >=0.11)

3. (medium) Centralized examples (from)

   1. (high) bespokefit protein-ligand or ligand-in-water example

4. (medium) Centralized OpenFF “book” docs

5. (medium) Toolkit docs cleanup

6. (medium) Toolkit revised user guide (+-unifying/centralizing package user guides)

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. (medium) bibtex blocks for website “how to cite” page on

9. (low) Propose policy for using GH citation machinery

10. (low) Check main website for broken links

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