relax SVN archive

Started to redesign the generic_fns.pymol module to use the pymol python package.

This involves much renaming of the PyMOL pipe object which is not the PyMOL executable object. This
attempts to use the pymol python package, and if not available PyMOL will be run from the command
line as a pipe.

Added the import of pymol modules to the dependency checks.

Removed the pipe check from the pymol.command() user function.

This is not necessary.

Bug fix for the generate_vector_dist() function.

The limits function was being called even if not supplied! This change fixes that.

Bug fix for back_calc_ri()!

The bug was introduced at r10967. The check for missing data was not performing correctly, causing
the Monte Carlo simulations to be stuck in an infinite loop!

Fix for the cone_edge() function for a non-zero apex position.

Various point distributions can now be used for the cone PDB representations.

This includes the original 'uniform' distribution and now the 'regular' distribution.

Renamed the pivot point to the apex in create_cone_pdb().

Bug fix for create_cone_pdb() for when a rotation matrix is supplied.

The cone central axis was not being rotated!

Bug fix for cone_edge() for when a rotation matrix is supplied.

The latitude points were not being rotated.