2020-07-28 Molecule Set Compilation

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.

        "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?

Provenance?

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

• Version Hahn’s molecules?

Future plans

• Making this part of release checklist in the future?

• Replacing mol2 with SDF in the future?