2022-06-08 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Let’s take the bespokefit optimize-then-single-point PR off your plate. SB indicated that it would need a more thorough rewrite and it’s not within our jurisdiction to lead new feature development.

  • JM – Sounds good. I left another comment a few days ago about another issue as well.

PR/Issue clearance

• (Discussion about in-progress PR 1314 and future steps)

Skunkworks notebook

• Should make it clearer when we’re calling Chemper

• JM – We should have perceive_residues update atom names.

  • JW – Good idea. Let’s add kwarg perceive_residues(overwrite_atom_names=False)

• JW – Since we’re a force field shop, it would be amazing to show the molecule in 2D or 3D, somehow showing where parameters get handed off between the protein and small molecule force field.

Todos

1. (high) Topology refactor polishing - details

2. (high) Skunkworks notebook - Force field blending visualization

3. (high) Topology refactor - better errors from PDB loading

4. (medium) Skunkworks notebook bespokefit integration

5. (medium) Centralized examples (from 2022-04-27 Mitchell/Wagner Check-in meeting notes

6. )

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

7. (medium) Toolkit docs cleanup

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

9. (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…”)

10. (medium) bibtex blocks for website “how to cite” page on http://openforcefield.org

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

12. (low) Check main website for broken links

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