Added docstrings in some QM classes

Attributes were not included in some of the base qm
classes. They are now.
Documentation: QM options in the input file

Hopefully this is clear. Highlighted the external programs
linked with QM (Gaussian, MOPAC, RDKit). Also gave an
example script to include in the input file.
Documentation: Added QM to the RMG API tree

Hopefully this won't change much.