RDKit change introduced some failing unit tests.

[rwest]

The change to RDKit (in #135) introduced/revealed some errors.
These can be seen in the automatic build robot's unit test log:
448e852#diff-6

They are mostly molecule and atomtype checking.

[rwest]

My series of commits this weekend has fixed most of these.
What remains is symmetry and thermo checking of benzene, because the unit test specifies it via SMILES='c1ccccc' and we Kekulize it when reading.