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.
JM – I’ll be finishing up my thesis in the coming days, so I may request time unpaid in the future.
JW – Thanks for the heads up. I’d approve that request, just let me know if you need it.
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.
(high) bespokefit protein-ligand or ligand-in-water example
(medium) Toolkit docs cleanup
(medium) Toolkit revised user guide (+-unifying/centralizing package user guides)
(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…”)