Added cmap parameter handling.
Added cmap parameter handling.

Rather rudimentary, as we store the cmap parameters as text files.
This might need to be included.  Additionally some changes to
make index handling consistent.

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