relax SVN archive

Fixed the call to relax_io.file_root in vector_dist().

Added the missing self argument to the clear_history() method.

Converted the clear_history() function to a method of the PyMOL data object.

Converted file_root() from a class method to a module function, and updated it to the new design.

Updated the cartoon() function to the new relax design.

Created a data container for storing the pymol command history.

Converted all the class methods into module functions.

Fixes for the pymol user functions.

The pymol module is now being imported and its functions being called. The class methods of
generic_fns.pymol still need to be converted to module functions for this code to work.

The geometric object functions have the correct args now passed into them.

The cone_pdb() method is now calling the geometric object functions in the correct locations.