Check QMTP optimized molecular geometries

The QMTP module was only checking if the InChI hash used for a molecule was not used by another molecule. This was done by checking that the InChI for that molecule was present in the output file. However this does not mean that the thermo found is correct, as the molecular connectivity could have been altered during the optimization. These changes get the molecular connectivity of the optimized molecule and match it to the RMG molecule via an isomorphism check.