relax SVN archive

Added code to the cone_pdb() function to generate the cone cap.

The generic_fns.structure.generate_vector_dist() doesn't exist yet though. A few print out
statements were also added.

Removal of a few comments.

Removed some debugging code.

The ave pivot-CoM vector is now correctly calculated, and the full length vect is now separate.

Renaming of a number of variables for the CoM analysis.

These names are more logical.

The length of the pivot-CoM vector is now being used to specify the size of the cone.

Bug fix in the CoM() function. The variable unit_vector was being referenced before it existed.

The pivot-CoM vector is now stored in the data pipe.

Bug fix for the cone_pdb() function.

The average pivot-CoM vector is now the correct length.

Deletion of the N-state model branch.