2022-05-18 Thompson/Wagner Check-in meeting notes

Owned by Jeffrey Wagner, created
Last updated: May 19, 2022
2 min read

Participants

  • @Matt Thompson

  • @Jeffrey Wagner

Discussion topics

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Notes

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Notes

General updates

  • JW – Annual meeting June 28 - I’ll probably hit you up for slides

    • MT – Sounds good. I have scipy two weeks later so I’ll reuse the slides.

  • JW – Bespoke release - Expecting a lumpy workload for user support. We’ll see.

    • MT – I wouldn’t stress too much. If there’s something seriously wrong we can battle-harden it and do another soft launch in a few months.

  • MT – What’s the future of bespokefit? Do we just keep it running in its current form, or will this become central to fitting team work?

    • JW – I don’t know. I think sage was made largely using an early version of bespokefit (or something like that). So I think that the fitting team may continue to use it heavily.

PR/Issue clearance

  • Bespokefit single file installers wrapup?

  • Are there valid cases in which a molecule will have multiple charge handlers applied to it?

    • JW – No

    • If charge_from_molecules applies anywhere, the molecule is done since it can only apply to the WHOLE molecule

      • JW – Yes

    • I can’t think of any useful cases in which library charges are applied to a part of a molecule but not the whole (ionic molecules, biopolymers, LibraryChargeType.from_molecule

      • JW – Yes. LibraryCharges only apply to a molecule if they cover EVERY atom

    • I can only think of cases in which ChargeIncrementModelHandler is applied to an entire molecule

      • JW – Yes

    • If AM1BCC is used, does it even make sense for the molecule to be a patchwork of the three charge methods?

      • JW – No

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0.11 release planning

  • PDB reading

    • Speed

    • Input diversity

    • Better errors (loudly yell about what we require from inptus)

    • Better docs (loudly yell about what we require from inptus)

    • from_rdkit/openeye (assigned stereo and aromaticity?)

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  • Examples

    • Protein FF finalization (should people be using the ff14sb port)?

    • “Happy path” for protein+ligand setup =

protein_interchange = ff14sb.create_interchange(protein) everything_else_interchange = sage.create_interchange(ligand_and_waters_and_ions) final_interchange = protein_interchange + everything_else_interchange omm_sys = final_interchange.to_openmm()

Notably, the recommendation on release day will NOT involve importers from openmm/amber/gromacs.

 

  • Migration guide

    • Units (done)

      • We can load OpenMM.units, but NOT simtk.units

    • Topology stuff/API breaks

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  • Downstream package releases

    • ForceBalance

    • BespokeFit

    • QC*

  • API cleanup

    • default hierarchy schemes

  • Topology positions/conformers

    • If all molecules have at least one conformer, Interchange will assume that that should be their positions. But if ANY molecule doesn’t have a conformer, then the Interchange isn’t built with positions

    • We will NOT add Topology.positions to the API (at least not now)

 

 

Action items

Decisions