User-defined dihedral angles for clustering?

[vvoelz]

The Voelz lab is currently building MSMs from simulations of non-protein small molecules and peptidomimetics that don't have the usual phi/psi/chi/omega, etc.

It would seem easy enough to add user-defined dihedral definitions by passing in a flat file of listing quartets of atoms (specified by residue number and atom name) -- this is something we have gotten to work before with an earlier hack. Maybe this would be a useful feature in general?