2021-05-14 QCA User Group meeting notes

Owned by David Dotson, created
Last updated: Sept 14, 2021 by Joshua Horton
3 min read

Participants

  • @David Dotson

  • Ben Pritchard

  • @Joshua Horton

  • @Simon Boothroyd

  • @Trevor Gokey

  • @Jeffrey Wagner

  • @Pavan Behara

Goals

  • Updates from MolSSI - Public QCArchive

  • User questions / issues, new submissions

  • Infrastructure needs / advances

Discussion topics

Item

Presenter

Notes

Item

Presenter

Notes

MolSSI - Public QCArchive

Ben

User questions / issues



  • DD: Simon, anything you need for industry benchmark dataset?

  • SB: no, I think these are just bugs on the toolkit side; nothing needed at this time on the QC* side

  • JW: toolkit behaves differently depending on when it sees mapped smiles vs. unmapped smiles

  • TG: noticed that the server availability appears to have decreased over the last few months; appears down for 10 - 20 minutes

    • BP: the public Fractal Server?

    • TG: yes, next time I get a ‘connection refused’ will reach out to see if we have corresponding activity in the public server logs

  • DD: Gen3 torsion set, technically ready to go

    • SB: haven’t had a chance to give it a look; let’s wait to submit this so we can give the industry benchmark set more time to complete

  • DD: Gen3 Opt set in preparation by Hyesu; where does this fit in priority?

    • SB: keep industry benchmark on top for now

  • JW: connectivity filter discussion: https://github.com/openforcefield/openff-toolkit/issues/936

    • SB: the filter I shared in the DM could be used to identify the cases in the dataset impacted by this issue

    • JH: course of action:

      • keep current dataset going

      • will have a QCSubmit download filter that handles cases like this

      • should also introduce a fix in the toolkit that throws errors when we encounter cases like this (basically, a validation error)

    • JW: believe we need to:

      • ensure that validation in openff-benchmark captures these cases, filters them out

        • probably requires toolkit fix

      • JH: for the QCSubmit filter (for export), can just look at the CMILES for any implicit hydrogens when hydrogens on the molecule are otherwise explicit

      • JW: action items

        • resolve toolkit issue

        • raise issue on openff-benchmark that CMILES such as this should be filtered out by validation component

      • JH: will go through dataset and try to get all impacted IDs

        • will inform the approach for the filter

Action items

@David Dotson will identify case in OpenFF Full Optimization Benchmark 1 in which result fails to parse in client, share with Ben, determine appropriate fix in PR against QCFractal
@Trevor Gokey will share with Ben the next time he sees a connection refused issue with the public server instance
@Joshua Horton will identify impacted IDs from OpenFF Industry Benchmark Season 1 v1.0 in which implicit hydrogens in the CMILES sit alongside explicit hydrogens
@Joshua Horton will create a QCSubmit filter for the implicit-explicit hydrogens CMILES cases, generally used for data export for fitting and other activities
@Jeffrey Wagner will identify cases exhibiting implicit hydrogens in CMILES alongside explicit hydrogens in the submission dataset; use these to inform how these should be handled in the toolkit
@Jeffrey Wagner will raise issue on openff-benchmark that CMILES such with a mix of implicit and explicit hydrogens (or really any implicit hydrogens) should be filtered out by validation component

Decisions

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