Allow user to specify list of atom indices to override default behavior for selecting the REST region

[zhang-ivy]

Currently the default behavior of the RESTCapableHybridTopologyFactory is to determine the rest region by selecting all atoms within a user-specified radius of the alchemical atoms.

It would be nice if the user could override this behavior to specify atom indices of their choice, independent of the alchemical atoms and a radius.

Considerations for implementing this:

• Since this function is part of the RESTCapableHybridTopologyFactory, the hybrid topology has not been generated yet, so the user will only have the old topology atom indices. We'll need to use self._old_to_hybrid_map to map the old atom indices to hybrid indices.