relax SVN archive

Updates for some of the Structure.test_create_diff_tensor_pdb_* system tests.

This includes Structure.test_create_diff_tensor_pdb_ellipsoid,
Structure.test_create_diff_tensor_pdb_oblate, and Structure.test_create_diff_tensor_pdb_prolate.
The new simulated PDB truncation in the test data causes the PDB files created in these tests to be
slightly different.

Reintroduced the simulated PDB truncation into the artificial diffusion tensor test suite data.

This is different to the previous implementation which was deleted recently. It now simulates the
truncation of both the N and H positions in the PDB and reconstructs the expected vector.

Python 3 fix for the generate_data.py diffusion tensor to relaxation data creation script.

The string.upper() function no longer exists.

Modified the generate_data.py diffusion tensor to relaxation data creation script.

The NH vectors are no longer truncated to match the PDB.

Python 3 fix for the lib.sequence_alignment.align_protein module.

The string.upper() function no longer exists.

Python 3 fix for the lib.sequence module.

The string.upper() function no longer exists.

Updated the Structure.test_align_molecules system test for the changed PDB structures.

The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the
atomic positions are different.

Updated the Structure.test_align system testt for the changed PDB structures.

The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the
atomic positions are different.

Updated the Structure.test_delete_atom system test for the changed PDB structures.

The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the
atomic positions are different.

Updates for the Structure.test_create_diff_tensor_pdb_ellipsoid system test.

The PDB checking has been updated for the new data.