Integrate hybrid topology factories into openmmtools

choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

http://openmmtools.readthedocs.io

MIT License

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Integrate hybrid topology factories into openmmtools #722

Open ijpulidos opened 11 months ago

ijpulidos commented 11 months ago

Current implementation of hybrid topology factories in perses are currently in a state that they could be integrated into openmmtools code base. Maybe an alchemy package/module that contains it (for example what has been proposed in the relative branch ).

Namely, this would minimally require migrating the HybridTopologyFactory and the RESTCapableHybridTopologyFactory into openmmtools.

IAlibay commented 11 months ago

Following up from discussions with @jchodera on slack - how would folks feel about a first pass of just moving the base HTF class without the TopologyProposal requirements into openmmtools?

We could take https://github.com/OpenFreeEnergy/openfe/blob/main/openfe/protocols/openmm_rfe/_rfe_utils/relative.py, make sure we merge in any new changes from Perses (I think cutoff modification hasn't been ported through yet). And then start iterating on refactoring the object model?