2022-06-01 Mitchell/Wagner Check-in meeting notes

Updates

• JW – The support email is finally getting emails from someone. Let me send you the credentials

  • JM was able to log into support email, but JW had to disable login challenges for 10 min using this page: https://admin.google.com/ac/users/1t3h5sf0yfhr18/security?hl=en

• JW – Nice catch on mutablemappings and python 3.10

• JW – Lily is now acting science lead

• JW – One spot I found in the docs that will fall out of date after the 0.11 release:

  • Cookbook: Every way to make a Molecule — OpenFF Toolkit 0.16.8+d20250225 documentation - Molecule.from_topology is no longer the best way - Can just do Topology.molecule(0)

• JW – What would be helpful in the coming week or two or three would be intense polishing of the topology refactor branch - So things like:

  • SHOULD BE BASED OFF https://github.com/openforcefield/openff-toolkit/pull/1306 (or wait until this is merged)

  • Better error messages when loading proteins (either OFF or OMM should raise a descriptive error about the following):

    • “This protein is missing explicit Hs”

    • “This looks like a modified amino acid”

    • “I don’t like this cap”

    • This can only be a single molecule in a PDB file

    • missing atoms/unresolved loops

  • Good tests could be:

    • a protein without Hs

    • A protein with a modified AA

    • a protein with unresolved atoms

    • a pdb with two proteins

    • a pdb with a protein and xtal waters (suggest how to separate them using eg. mdanalysis or pdbfixer or something before loading)

• Make hierarchy get perceived when you run perceive residues, in other words:

• ala_cysdye_ala.perceive_residues() ala_cysdye_ala.add_default_hierarchy_schemes() ala_cysdye_ala.perceive_hierarchy()

  should be refactored to

• ala_cysdye_ala.perceive_residues()

Todo

1. (high) Review

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

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

3. (medium) Toolkit docs cleanup

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

5. (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…”)

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

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

8. (low) Check main website for broken links

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