Allow user to specify list of atom indices to override default behavior for selecting the REST region
zhang-ivy opened this issue · comments
Ivy Zhang commented
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 useself._old_to_hybrid_map
to map the old atom indices to hybrid indices.