2024-12-16 Science team meeting

Project updates

BW

• Last week

  • QCA workers

    • lipid-maps-medium

      • Wrapping up soonish

    • lipid-maps-large (on virginia tech)

      • deprioritised in favour of organometallics

  • Organometallics dataset

    • Will merge and hopefully get data for ML TM meeting

    • JCl and I met earlier to transition

  • Protein benchmarks

    • Still getting NaNs

    • LW: when did it crash? should be in *.out file

    • goes up to 156399 ps

  • nagl2

    • JCl: the README or gen needed a description for the NAGL2 dataset

    • (Gen): the script updates the description later in file

    •  

• Next week

  • Off-boarding:

    • Meeting with JE is exit interview

    • Meeting with JW (Fri) is account closure

    • curato, lipoma, benchmarking, vflib2, qcaide

    • make sure dfs9 is rw-able for everyone in the group

      • LW: only checked subdirectory

    • big datasets should be uploaded to zenodo or google drive

      • fragment database/s

      •  

    • Projects

      • Torsion multiplicity

      • Torsion profile target in ForceBalance

        • restrained-torsion-profile:

      • FF fits for Trevor

        • Nothing further since v3

      • Smee fits

        • reran with scaling factors, fcs still went to 0

        • /dfs9/dmobley-lab/bwestbr1/descent-ff/energy-force/scale

      • dfs9

        • valence-fitting: TM work

        • refits:

          • restraint: restrained FB work

Project updates

JCl

Past week:

• CMILES Issue: [H][NH+][H][H] has not implicit hydrogens in RDKit, but found that also doesn’t have all “explicit” hydrogens in graph. This is resolved with a test.

• First sage dataset done, needs to finish review

Next week:

• Working more on CMILES issue: Suspended until the new year. Need to go through GitHub issues

• Dataset release stuff

  • Finish Sage

  • Industry Benchmarking dataset

• CIF parsers:

  • gemmi, other cif parsers

    • https://gemmi.readthedocs.io/en/latest/cif.html

    • https://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html

  • Does BW have statistics for CCD?

    • BW: some of the filtering code in my repo could be used for this

    • Set up a pair programming session

    • Jeff is also a good resource

    • CIF also has bond orders, so possible to assemble rdkit molecule

  • QCA-DS

    • Uploading to Zenodo

Project updates

LW

• Past week:

  • Looking into Evaluator liquid simulations

• Next week:

  •