Updates since last meeting | JW – I’ve been drawn off to a lot of other small things the past several months. I resolved the big merge conflict for the topology refactor branch, and I’m close to pushing a branch with HierarchyElements/Schemes that fulfills our aspirational API from earlier. IP – Perses team has identified some spots where aspirational API may not be aligned with needs, or where functionality may not be possible in a timely/safe way. IP – Many Perses users won't need the cheminformatics representation of a molecule. They’ll just want to know stuff like the number of residues. JW – That sounds like TypedMolecule, which is basically a networkx graph. Are there specific parts of functionality that will be helpful for users there? IP – If we have a reliable perceive_residues, then users should be happy. But it seems like perceive_residues will be really hard. And there will be a lot of cases where people load a molecule that ALREADY has metadata, and just want to iterate over molecules. JW – We should make sure that TypedMolecules play nicely with HierarchySchemes/Elements, so that users will be able to make use of them without doing any residue perception. IP – Espaloma will eventually need to know residues. So that is also a good long-term goal. JW – I’m excited for espaloma support, but OpenFF is totally backlogged and gathering technical debt right now. So we need to finish off our 2021 deliverables before we formally support espaloma. I’m happy to spend 4 hours with Chodera lab folks to get a prototype plugin working, but we really can’t begin getting it into the core toolkit until 2022.
IP – Is ParmEd still the best way to combine systems?
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