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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 MT will look into making functionality to do 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 Assume that the ff is loaded as ForceField('openff-2.0.0.offxml','ff14sb_off_impropers_0.0.2.offxml'), and the user will call the _unrecognized... command chain between loading the FF and creating the system.
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. MT will work on AMBER loaders that can take “simple” systems, like
Test usage of graph_tool 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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