Return parent fragment mapping

[jthorton]

During the QCSubmit call today we talked about validating highlighted dihedrals for torsiondrives and found that it would good to check the dihedral is correctly identified by returning a mapping between each fragment and the parent.

[SimonBoothroyd]

After #68 each fragment should contain a "atom_map" dictionary in the properties field which contains this map.

[ldamore]

I found that the atom mapping of the fragmented molecule is rearranged with respect to the parent molecule. Could this be avoided? Or should this be documented? I just opened the issue #126 for this.