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Notes

General updates

Roundtable updates

  • JW –

    • Worked on ring stereo/pseudosymmetric representation problem - Looks like we should be able to make it work

    • Some molecule sanitization/canonicalization work for benchmarking - OPLS “sanitizes” inputs to have different graphs in some cases, like [S+2]([O-])([O-]) → S(=O)(=O), which breaks our analysis workflows. Used MolStandardize.rdMolStandardize.Normalize(rdmol)

    • Biopolymer topology refactor – Implementing quick molecule-identity checks, incorporating into parameterization loops.

    • Worked with AMBER dev (Kellon) to standarize on CCD

    • Roadmap revision is done, except espaloma question and some biopolymer benchmarking details

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