Class GroupByConnectivity

Groups the atoms by molecule connectivity. Returns a list of atom groups.
Each group is a list of atoms that are in the same molecule - 
that are bonded to each other, counting only atoms in specified list.

After creating the instance, you gen get the resulting list of atom groups
by calling the groups() method. You can also do:

for atom_list in GroupByConnectivity(st, all_atoms):
    <work on atom_list>

NOTE: atoms list should NOT contain duplicate atom number entries