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Date

Participants

Goals

Discussion topics

Item

Notes

Progress reports

Dotson

  • Nothing yet – Onboarded last week

Thompson

  • Not a ton – Onboarded last week

  • Worked on #551 to implement parameterhandler.get_parameter – Needs review

Boothroyd

  • Worked on mixture feasibility studies, working on codebse for surrogate mdoeling

Horton

  • Defended thesis

  • Adding CMILES functionality to OFFTK – Needs review?

  • Adding state enumeration, available in newest release of RDKit

  • First draft of QCSubmit working. Need to set up Travis testing.

Hahn

  • Worked on free energy difference workflow – “PMXWorkflow”, based on de groot scripts. Original code needs refactor, new workflow not yet public. Some question about “ownership” – I am not free to give it away, since it’s not clearly mine. Would like to post somewhere public.

  • Continued on PLBenchmark repo

Wagner

  • Onboarded new SSs and Cerutti

  • Working on SDF charge I/O. SDFs are complicated and not isomorphic to OFFMols.

    • SB – Pick one serialziaton format for OFFMols on disk

    • DD – A C++ codebase would be able to read a standard serialization format. Or other projects could use a python interoperability layer to load our molecules

    • SB – We should stick with objects being in one language

    • JW + SB – If we use Pydantic to define our object model, we should be able to dump out a language-independent schema represenataion of our data structure.

    • DD – Agreed

  • Working on chargeincrementmodel PR – Need to check with Yuanqing.

  • Working with Gokey on virtualsite support – Expect changes to Topology and Molecule

Jaime

  • Negative feedback from c-f on policy proposal for openmm compatibility

    • This is kinda good, since now we can talk with PKE about moving forward with a specific openCL management model

Task delegation

  • Jeffrey Wagner – Cerutti support

  • Matt Thompson Take over dev docs branch

  • Jeffrey Wagner #281, Chargeincrement PR. Torsion WBOs

  • David Dotson #305, #379, #381

  • Matt Thompson (primary) David Dotson (secondary) QCA OpenMM energy evaluation

    • Should run MM energy calculations in QCA – Do we want to run on existing QM geometries, or regenerate torsion scans using MM ffs?

      • Probably start with QM geometries

      • If possible, should run evaluations in QCA

    • Check for connectivity rearrangement?

      • Would be nice

      • Could use WBO cutoff to detect connectivity

    • Josh’s offmol.from_qcschema can do much of this

  • David Dotson (primary), Matt Thompson (secondary). Start on knowledge transfer for OpenFF Evaluator handover → Assign a few issues

  • Matt Thompson Appoint a git branching investigator (Due mid-april / new model adopted starting at 0.7.0 release)

    • Will present on tradeoffs of each strategy, and drive a vote on Monday

    • SB – would be good to copy a model from community if possible (scipy, DASK, numpy, etc). Also I’m against having a continuous RDKit-only dev branch, and OE-also dev branch.

    • JRG – Initial reviews could be RDKit-only. Then we have a second internal step on an internal branch, and opens a second PR that depends on the first (where we test OE). Intermediate branch could be temporary.

    • JRG – Maybe we don’t need a second PR branch for OE. If we migrate to GHA, we could use metadata in the PR to accept

  • Slay the OpenEye license/branching beast

    • Couple with transfer of CI to GHA?

      • No

    • Probably want an “RDKit-only” contributions branch

    • Automation so that a malicious user can not open PR into master/access oe_license

    • Policy for accepting OE-only features (never allow? Require RDK equivalent?)

  • Jaime Rodríguez-Guerra (Deactivated) Migrate OFFTK CI to GHA



Action items

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Decisions

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