Page Comparison

Fitting mols

• Convert all 1.2.0 release tarball mol2s to SMI, then those to PDF

  • HJ – We wouldn’t have used ALL of the torsions in the structures in our torsiondrives.

    • Could highlight driven torsions eg.

      Code Block
      "entry_label": "c1cc[c:1](cc1)[CH2:2][N:3]2[CH2:4]CCCC2=O",

      in fb-fit/targets/td_OpenFF_Gen_2_Torsion_Set_1_Roche_2_020_C12H15NO/metadata.json

  • Will all vibration frequencies be present in optimizations?

    • Unlikely

• Separate by data/QC job type?

  • Make two pdf and smi files – One with all unique molecules (period), and another with molecules separated by data type, and highlighting driven torsions.

    • Let’s take the low-hanging fruit first (just list all unique SMILES and 2D structures), and get more elaborate if people ask. Scrolling through ~20 pages of highlighted torsions isn’t feasible anyway.

• Identifier in PDF, which is also attached to SMILES

  • Name? SMILES itself?

  • Try doing SMILES in really small font, and only have three or four rows, so that people can Ctrl-F for their molecule of interest in the PDF.

• What’s the best way to make benchmarking 3D structures available?

  • The set is hard to wrangle (due to overlap with fitting data), so let’s not worry about 3D structures initially

Benchmarking mols

• Just repost Hahn’s molecules

  • Are these the same as in benchmarkff?

    Github link macro
    link https://github.com/MobleyLab/benchmarkff/blob/74f500241810cdfc99ead0392d8ea0be5e93cb00/molecules/molecule_PDFs/molecules.pdf

Provenance?

• Record process for converting 1.2.0 release package to SMI/PDF

  • Where? How?

    • versions-- at least conda env export

    • List steps in the website PR? Paste script?

    • Upload script/smiles/pdf of this set to release assets?

      • No. Those should be immutable.

    • Attach to a new release of one of our repos? New repo?

    • How do we handle stuff like this? It’s always done ad hoc

    • We NEED some simple, consistent dataset guidelines!!! Uncertainty here adds a ton of effort and builds institutional debt!!!

• Version Hahn’s molecules in case we update dataset?

Future plans

• Making this part of release checklist in the future?

• Replacing mol2 with SDF in future FB fits?

  • HJ will look into this