Item | Notes |
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Task planning | Can move ahead with reference dataset, even if some details aren’t hammered out in the SMIRNOFF spec – Lots of peolpe just want to know if they’re getting torsions right, don’t care as much about precise agreement with long-range forces Capping+charging unrecognized AAs in a protein. LibraryChargeHandler.unrecognized_contiguous_subgraphs → list of tuple of atom indices?? Then we could have a way to turn those subgraphs into capped mols, assign charges, and turn them back into LibraryCharges??
May be good to get interface hints here from LWang’s polymeterizer
Interchange importers? MT – Blocked by lack of TypedMolecule, could use mdtraj top as a crutch for now. MT – Concerned about scope creep. Some things are black and white - Loading a prmtop that uses ff03 should clearly be allowed, loading a prmtop wiht an unsupported vsite is clearly not our job (though folks are free to open PRs). But there’s a significant grey area around things like loading CMAPs from prmtop.
Test usage of graphlib instead of networkx for heavy comparisons in Toolkit is/are_isomorphic → Relatively cheap, ok to be inefficient. Only expected to match entire molecules. SHOULDN’T try to match subgraphs. Less important to remove networkx here.
Molecule.from_pdb → Very expensive, could be sped up a lot. Needs to match subgraphs (individual residues in a larger chain). Important to find something faster than networkx here.
Somehow improve SMARTS based parameter assignment for proteins. This would be really easy with multiprocessing, but that’s the last tool I want to reach for.
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Units PR | MT – When can we stop supporting simtk.units? It adds a good amount of complexity to openff-units. JW will finish reviewing this on his own time – Logic looks good, will just act a s a second set of eyes for typos. If #1097 look good, we will close it and merge #1142, since it’s the same logic, just ported to the topology-refactor branch.
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Topology performance/molecule grouping merge | |
Pushing molecule grouping updates into interchange | |
Topology-export-to-different-format needs | |
Resolving positions debate | How many conformers can a molecule have? Can a Topology have conformers? What is the relationship between interchange positions and molecule conformers?
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