Allowed RDKit to read PDBs only when combined with a valid smiles string, this adds a new classmethod from_pdb.

This introduces new functionality for `are_isomorphic` function which now can return an atom_mapping and can match based on user criteria.
This will be useful to refactor `Topology.from_openmm`.

hill_formula implemented

to_qcshema implemented
from mapped_smiles implemented with internal atom ordering remapping.

from qcshema started from cmiles only using an instance.

Author: joshhorton