2022-09-14 Mitchell/Wagner Check-in meeting notes

General updates

• PERMANENT: Sprint planning

  • Done

• JM – I think there’s a problem with Molecule.from_pdb_and_smiles

  • (Worked on it for a while, JM was right, and the test cases that we happened to be using just had symmetric molecules like toluene where this issue would be hidden)

• JW – Assistance planning workshops?

  • JM – There’s a lot of jank in the PTM handling notebook around connecting the molecule and defining the library charge

  • JW – I think the smiles modification step is jankier - I wonder if the molecules could be merged in rdkit instead.

• Bespokefit PR

  • (JM prodded at remaining comment)

• JW will have lead team start running tea times for OFF time zones.

Todos

1. (high) Resolve feedback on BespokeFit PR and make discussed change

2. (high) Prepare material for Bespokefit workshop (materials from last time)

3. (high) Prepare material for PTM/advanced toolkit use workshop

4. (medium) Update bespokefit to work with Toolkit 0.11.0

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)