Refactor the input file writing

This is quite involved. There are different input files
that need to be written for the transition state search
methods. They were mostly written for b3lyp/6-31+g(d,p),
but as a method and basis set variable has been added for
each method, they have now been generalized for use by all.
Use parseFILETYPE methods created in qm.molecule.Geometry

Remove redundant code and use the methods created that
does the job. Also allows a singe method to write the
input files since the outputs from these parsing methods
are standardized.