2025-01-27 Science team meeting

Project updates

JCl

Previous Week:

• TM-FF

  • DS1-PDB CCD:

    • of the 154 structures in the primary dataset, ?? make it through the xyz2mol script.

    • Tried again to adapt script to have a timeout so that a manual exclude list isn’t needed for larger datasets… that still isn’t working

  • DS2-COD

    • Finished draft of parsing scripts…but now not confident that the contents are relevant

  • DS3-CCD

    • Access update? Maybe skip it

    • Paper only directs readers to tmQMg repo with ~75k “structures“ (xyz files)

    • The xyz2mol_tm repo contained SMILES for tmQMg and ~220k structures of CSD.

    • We can:

      • Take xyz files and smiles for ~75k * 0.7 of tmQMg

      • Use cleaned CSD SMILES to generate dataset of ~220… recall that geometries are bad… can we use UFF to fix? (like Avogadro does)

  • Sent message to EPA contact about ToxCast, haven't heard back.

  • Consider looking at other databases?

• Dataset Longevity

  • Discussed in “iteration planning” I said it was a lower priority with the current issues. ok? I’ll continue chipping away if other tasks stall before I can request assistance

• NRP Issues

  • Still not resolved. Applied python API to isolate that it’s a MolSSI issue, messaged Ben today and he’s looking into it

• Given QCSubmit datasets haven’t moved due to NRP issues, cancel meeting? Is Shirt student attending? Seems so.

Project updates

LW

• Past week:

• This/next week: