Iván Pulido

While dealing with issue #993 I realized that the `platform` gets changed along the way for some of the tests. In general, I think this is something that needs improvement....

It is desired to extract trajectories fro perses results for visualization and validation purposes. An API point in the `perses.analysis` module could hold this functionality. We can use @zhang-ivy [shared...

From https://github.com/choderalab/perses/issues/863 it was noted that it is possible to gain some performance by optimizing `_constraint_repairs`. It might worth doing it for larger systems.

Profiling setup workflows

3

Identify bottlenecks in the setup steps by profiling.

We need to check we are using the context manager for temp dir and files all over the code base, we are seeing some CI errors such as https://github.com/choderalab/perses/pull/787/checks?check_run_id=3769983560

Remediate OpenForceField protein-ligand benchmark PDB files

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Remediate OpenForceField PDB files

Output compounds SDF files with experimental and computed affinities.

1

Support specifying experimental absolute free energy values in specific SDF tags for the compounds. We will need to standardize the tags and the units.

Examine Alchemical forces into separate Force Group for `RestCapableHybridTopology`

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CC #848 Examine Alchemical forces into separate Force Group for `RestCapableHybridTopologyFactory` The NonBonded force that handles env env interactions can be in its own force group.

Add examples that Interline folks provided. Link to follow.

Support cofactors ("spectator ligands") in SDF format can be with full 3D coordinates. This would probably require a new option in the configuration YAML file of the simulation.