Remove CML from example input file.

Without OpenBabel we cannot read CML.
If we re-enable it, revert this commit.
Tweak the molecule drawing - make bonds a little shorter.

I think this looks a little better, at least on the molecules I tested it on.
Get the qm.molecule.rd_build to use the molecule.toRDKitMol method.

This reduces a lot of code repetition, although there were a couple of
minor differences between the methods. Namely:
 1) in the QM module we need to return a dictionary of mappings
 2) in the QM module we need to keep hydrogen atoms