relax SVN archive

Bug fixes for the new lib.structure.internal.coordinates.common_residues() function.

This function for determining the common residues between multiple sets of pairwise alignments was
failing in quite a number of cases. The logic has been updated to handle these.

Fix for the sequence alignment for assembling atomic coordinates.

This caused the Structure.test_superimpose_fit_to_mean system test to fail. The problem was in the
new logic of the lib.structure.internal.coordinates.assemble_coord_array() function. The coordinate
assembly now terminates when either the end of the first molecule or the current molecule is
reached.

Docstring update for the pipe_control.structure.main.assemble_coordinates() function.

This is for the algorithm argument which can now be set to None.

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.