RMG is unable to recongnize different kekule structures of aromatics

When RMG algorithim was changed to convert aromatics to S,D bonds
there was no check put in place to recognize different kekule structures
to be equivalent which resulted sometimes in two naphthalenes in the
mechanisms. For now I have added aromaticGraph and changed getSpecies
and putSpecies to check for the aromaticGraph also (rather than cycling
through all kekule structures ... the later might be more general test and
).

The current implementation works for when the species are in cache (checked
it by extending it to 5 from 2) but fails when it calls the
dictionary.get(p_chemgraph).