2022_08_25 Davel/Wagner check in

General updates

• CD – This is our last meeting within summer fellowship (ends on 31st).

• JW – We’re putting together a new roadmap that will determine how much we need to go full-speed toward industry requests vs. remaining largely involved with academic labs for longer-distance stuff. So the scope of my involvement in this project may change in the next month.

Previous to-dos

• CD will extend notebook to get all the way to simulation for one monomer. This will use gasteiger charges, and will warn users that these charges are not suitable for real work (it will provide a link to the LibraryCharges docs for further work). The substructure dict should be provided for that monomer, in case the user doesn’t want to run the previous steps.

  • CD – I’m having trouble with with unassigned torsion parameters

  • (JW + CD worked together, found it was due to formal charge not getting propagated to the final structure)

  • Progress is here:

• CD will make “unrecognized atoms” visualization only highlight things that can’t be recognized by ANY tiling of substructure, not just ones that aren’t recognized by the best tiling.

  • Done

• MRS will generate a list of PDBs that we can experiment with loading+minimizing

  • Done