Have Molecule.canonical_order_atoms optionally return a mapping from the old to the new atom order

[j-wags]

This would unblock an important feature in fragmenter. Full description at openforcefield/openff-fragmenter#129

I think the best way to do this is to thread a new kwarg through Molecule, RDKitToolkitWrapper, and OpenEyeToolkitWrapper's canonical_order_atoms methods.

[SimonBoothroyd]

+1 to this, and also, ensure that map indices survive the trip through this method. See also here for an example implementation.