Iván Pulido

I think it could be worth it to have this in a separate flow (yet another one haha). Is that a reasonable way to do it?

I don't see any immediate risks with this. I agree with adding it to the matrix (single python+linux).

This is still a work in progress. Since this changes the API we need to adapt the tests and examples that are affected by this change.

This requires refactoring the objects so that they accept atom maps instead of generating them on the fly.

Wwe could also try https://github.com/michellab/BioSimSpace/blob/devel/python/BioSimSpace/Align/_align.py#L719 caveat: I think it uses interconversion of the RDKit mol to a SireMol to get to the atom mapping. This may not be ideal

> @ijpulidos we're doing a lot of work on the openfe side to add new mappers (lomap, kartograf, and others eventually). Would it not make more sense for perses to...

Time machine mapper is in https://github.com/proteneer/timemachine/blob/master/timemachine/fe/atom_mapping.py

We should do the same validation as we do with the other parameters here https://github.com/choderalab/perses/blob/53c61b8bfddd6f815d2e4523af5d8c77eba030d8/perses/app/setup_relative_calculation.py#L1076

Just to note here that part of the difficulty is that the perses CLI withthe whole pipeline is not really meant to be run using MPI (it doesn't handle an...

@jchodera Can you please review this one? Thanks!