relax SVN archive

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.

Fix for the internal PDB structural object.

The data object is now initialised to an empty dictionary as in the base class it was initialised to
an empty list (causing the object methods to fail).

Added the missing import of the API base class.

Removed the initialisation of the 'atomic_data' structure in cone_pdb() as it is no longer used.

Updated the cone_pdb() method to use the internal PDB structural object.

Updated all the calls to atom_add() and atom_connect() to use the API methods instead.

Changed the 'atomic_data' arg in all the geometric function to 'structure'.

This is because the structral data object will be passed into these functions instead.

Added the atom_loop() prototype generator method stub to the structural API.