Consolidate duplicated code

[benmwebb]

e.g. get_particles_from_superposed_amb is largely cut-and-paste from get_particles_from_superposed; the two functions should be consolidated.

[shruthivis]

Confirmed that the pairwise calculator in pyRMSD can account for symmetric groups. So removed duplicated code. The other duplication is in rmsd_calculation.py (get_rmfs_coordinates_one_rmf and get_rmfs_coordinates). The latter is not supported any longer but retained for legacy reasons e.g. to support the actin tutorial. It may be removed in future versions of sampcon.