Massive redesign of the Scientific Python structural object atom_loop() method.
The new structural data data structure is now handled, and a number of changes have occurred to the
class methods:
__molecule_loop() has been deleted.
__residue_loop() has been heavily modified.
The method __ave_atom_pos() has been added to allow the ave arg to atom_loop() to be handled.
The molecule type is stored in the molecule containers by load_pdb().
