relax SVN archive

The rotation matrix is now calculated in the cone_pdb() function.

This avoids duplicated code in the generic_fns.structure module.

Modified the cone_edge() function to accept a rotation matrix as an argument.

Changed the residue numbering for the cone models.

The numbering is now:
1: Pivot point.
2: Average pivot-CoM vectors.
3: Cone outer edge.
4: Cone cap (for diffusion in a cone).

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.