relax SVN archive

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.

Docstring fix for the atom_loop() generator method.

Removed a line of debugging code.

Fixes for the centre of mass function.

Bug fix for the atom_loop() API generator method.

Wrote the atom_loop() API function for the Scientific Python PDB structure object.

The centre of mass function now works if the sequence does not exist in the current data pipe.

The spin_num and spin_name have been renamed to atom_num and atom_name respectively in the function
as well.