relax SVN archive

Fixes for the molecule name variable in MolList.add_item().

Fixes for the molecule name variable in pack_structs().

Fixes all over for the angles system test.

The sequence is no longer loaded as it doesn't have the molecule name and clashes with the
structure.load_spins() call. Hence the spin specific checks have been updated.

Fix for a call to structure.read_pdb() in the system test script.

Found and fixed the biggest pain in the ass bug ever (after 2 days of debugging)!

The model-free model index 'model_index' which was being passed into duplicate_data() was being
overwritten by the loop over structural models, which was also using 'model_index'!!!

Indentation fix.

A fix for the __parse_mols() method.

The 'END' PDB record is no longer identified as a molecule!

Bug fix for the MolList.__repr__() method, the molecule name is in 'mol_name'.

Missing import.

Fixes for the create_run() and execute() functions for the new structural data design.