Integrate new atom mappers

[ijpulidos]

We should be able to integrate other atom mappers such as the TimeMachine mapper or similar, that we could use in perses for doing the mapping.

[ijpulidos]

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

[ijpulidos]

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

[IAlibay]

@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 instead directly plug into those mappers?

[ijpulidos]

@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 instead directly plug into those mappers?

Yes! That makes a lot of sense.

[ijpulidos]

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

[IAlibay]

cc'ing @richardjgowers

[richardjgowers]

@ijpulidos you should probably think about Licenses if you're looking in BSS. And yes if you refactor so that the AtomMapping is an input then it will be relative easy to get this from Lomap/Kartograf/etc, I think wrapping up TimeMachine's approach is interesting, it's a more modern look at what rdFMCS can do compared to other options.