relax SVN archive

A number of fixes for the new generate_vector_dist() function.

Shifted the code for generating the diffusion tensor geometric object into generate_vector_dist().

The code has been abstracted so that it can also be used to generate cone caps, or any other PDB
objects which can be generated by rotating and warping a sphere.

The inc value has already been set as a variable, so no need to replicate the number in cone_pdb().

Bug fix for the cone_pdb() function.

The rotation matrix args are 'R', not 'rotation'.

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.