relax SVN archive

Changed the gap opening penalty to 10 in the N-state model structure_align.py system test script.

The pairwise sequence alignment is now active in the structure.align user function.

This is implemented in the lib.structure.internal.coordinates.assemble_coord_array() function for
assembling atomic coordinates. It will also automatically be used by many of the structure user
functions which operate on multiple structures.

The atomic coordinate assembly logic has been completely changed. Instead of grouping atomic
information by the molecule, it is now grouped per residue. This allows the residue based sequence
alignments to find matching coordinate information.

The assemble_coord_array() function will also handle the algorithm argument set to None and assume
that the residue sequences are identical between the structures, but this should be avoided.

A new function, common_residues() has been created as a work-around for not having a multiple
sequence alignment implementation. It will take the pairwise sequence alignment information and
construct a special data structure specifying which residues are present in all structures.

The logic for skipping missing atoms remains in place, but it now operates on the residue rather
than molecule level and simply uses the atom name rather than atom ID to identify common atoms.

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.