2023-04-20 Mitchell/Wagner Check-in meeting notes

General updates

• JW — Industry person recommended adding “you can calculate am1bcc charges and write them to a sdf” to an example

• JW – Working on Topology.from_pdb, just got lots of little fires to handle. I’m making it a warning instead of an error, squelchable with _ignore_stereo=False kwarg

• JW — We have a little bit of an emergency with the industry talks for the annual meeting - one of our top candidates may need to drop. Mind if I volunteer you to polish their code/improve their workflows? I may dispatch you to polish this code to entice them to talk/release them. It would be really cool to get them running with the nagl prototype and using topology.from_pdb with a sneaky _additional_substructures kwarg I could add

  • JM – Ok, this sounds great. Additional substructures in particular seems cool.

  • JW – I’ll send an intro if they take the offer, but one person is Rebecca Alford (J&J) and the other Daniel Smith (FL83).

• Talk prep

  • Maybe JW and JM can do the entire talk - JW will talk to MT about whether he wants to talk about Interchange and Benchmarking, or if JM and JW should run the whole thing.

Trello

To dos

1. (highest, due next Jeff meeting) Outline talk slides (can be just bullet points, just get concepts/timing roughly chunked out)

2. (high) Centralized OpenFF “book” docs

3. (high) Centralized examples (from)

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

4. (medium) Toolkit docs cleanup

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

6. (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…”)

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

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

9. (low) Check main website for broken links

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