Set the output file paths and give the molecule/reaction

A QM calculation is only going to be done on a molecule
or a reaction (TS calculation). This information is
useful for setting up the folders.
Attach the QMMolecule or QMReaction to QMCalculator

The RMG_bin path is also checked earlier, so that the
exception is caught before anything else gets done.
Correct the mainTest to handle the refactored main
Rename `setDefaultOutputDirectory` to match qm/main

Changed to `setOutputDirectory`. Subpaths are now
created within the qm output directory, so it is not
just set if the fileStore was not provided.
Use SMILES instead of InChIKey for qm uniqueID

With RDKit's canonical SMILES implemented, use this to
represent the file names and folders. InChIKeys are not
always unique.
Update gaussianTest and mopacTest to work with updated qm methods