2022-08-24 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Lead bespokefit workshop? JHorton will support but not lead.

  • JM – I could run this, with JH’s support.

  • (Scheduled for Oct 19 (EU + AUS friendly) +25 (AUS+USA friendly)

• JW – Sprint planning

  • (Done, updated to-dos below as well)

• JW – Bespoke PR

  • JM – No movement on this yet

  • JW – I’ve pinged JHorton and will take over as reviewer if I don’t hear back.

• JW – Thanks for jumping on support email

  • JM – No problem. It was mostly Matt

• Final release countdown

  • JM – I could use a few more hours

  • JW – I definitely won’t cut it tonight, but there’s a nonzero chance that things will be ready tomorrow.

  • JM – Ok, I’ll signal when it’s ready to go.

  •  

Possible last second changes

• JM:

  • del atom.name?

    • Let’s do this during meeting

    • atom.name must be set to a string, cannot be None: use empty string instead

    • This is already implemented, no action needed.

  • Fold Particle into Atom?

    • JW – No

  • Add missing TopologyMolecule API points to Molecule? eg, Molecule.atom(idx)

    • JW – I think this one exists, though it could have been lost in a merge conflict?

    • JM – Ah, looks like it exists.

    • JM – I can check for other things like this

    • JW – I don’t think I’d accept PRs for these before the 0.11.0 release, given that we can just merge them later (API extensions are fine after 0.11.0)

  • Atom.element_name?

    • JW – No

  • Deprecate Topology.reference_molecules, or use it as a way to iterate over unique molecules?

    • JM+JW – We should add an API point called unique_molecules, and then have reference_molecules could just emit a deprecation warning and return the output of unique_molecules

    • (JW+JM pair programmed )

  • Argument docs on create_openmm_system

    • JW – That would be nice - Mention that the underlying handler Document charge_from_molecules, etc. The real list should come from here in the Interchange docs.

  • Deprecate/remove ParameterHandler.create_force?

    • JW – Yes.

Todos

1. (high) refactor toolkit showcase to not use ParmEd/OMMFFs

2. (high) Resolve

3. (medium) Skunkworks notebook bespokefit integration

4. (medium) Prepare material for Bespokefit workshop (materials from last time)

5. (medium) Centralized examples (from)

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

6. (medium) Centralized OpenFF “book” docs

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

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)