New DesmondParser.py - now with more correctness
New DesmondParser.py - now with more correctness

DesmondParser.py should now work in most cases, except
for the dihedrals, which are not converting correctly.
A number of cleanups tasks were also performed.

ctk3b/InterMol,ctk3b/InterMol,shirtsgroup/InterMol,shirtsgroup/InterMol,mrshirts/InterMol,mrshirts/InterMol