2022_01_26 Mitchell/Wagner check-in

General Updates

• Need eyes on anything?/PR clearance

  • JM – https://github.com/openforcefield/openff-toolkit/pull/1180/files

  • All other PRs are failing because of a little RTD thing, this will fix it)

  • JW – It’s fine to merge any other approved PRs if the only issue is that docs are failing due to the above issue.

• JM – Need SB’s input on the ELF thing, since it may affect charges

• "How to cite" section in README, including Chaya's papers

  • Chaya “invented” fragmenter, and that has its own repo, so it was easy to give it a badge

  • But Chaya also studied wiberg bond order based interpolation, and that isn’t a standalone piece of software, so I’m not sure how to direct people to cite it.

    • Could make the toolkit print on a special logging level that people can activate to get their citations

    • Could add a page to the docs (under Getting Started)

    • Could have a “how to cite” page on the main website

      • Would need to have:

        • How to cite FFs (use table in this readme)

        • How to cite main software (Zenodo DOI) and SMIRNOFF paper https://dx.doi.org/10.1021/acs.jctc.8b00640

        • How to cite special features (WBO interpolation)

• Advice on placing + formatting a Molecule attribute conversion table in docs - https://github.com/openforcefield/openff-toolkit/issues/135 and https://docs.google.com/presentation/d/1sV4CQ5bORuAKy2q8TUJvaSVf2SI5Dy8HS8b-S7TsVis/edit#slide=id.g10f52e3ef1f_0_0

  • JM – It would be best to add a page to the Using the Toolkit section, like “Converting molecules between representations”. This will be good to surround with some text to give context for folks who aren’t experts, but are making a workflow, and it will provide an explicit central defintion of our “spec” for discussion of practices+changes. The docstrings or comments in the appropriate tests should point to the table.

• JM – I’d like to spend a few weeks doing a major cleanup of the OFF Toolkit API. I’d also like to clean up the library/module structure, and make things accessible from the top level (like, from openff.toolkit import ForceField)

To-dos

1. (high) Bespokefit users guide (in progress)

2. (high) QCSubmit users guide

3. (high) ELF10 COOH conformer rotation issue

4. (medium) Toolkit API desire paths, docs cleanup, revised user guide (targeted to biopolymer refactor branch)

5. (medium) Review+approve+merge OFFTK #1176

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. (low) “How to cite” section on website (do not start, pending feedback)

8. (low) Check main website for broken links

9. (low) migrate docs to be under http://openforcefield.org

10. domain (openforcefield/status would be base project repo)

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