relax SVN archive

Updates for many of the Diffusion_tensor system tests.

This is due to the changed directory names in test_suite/shared_data/diffusion_tensor/. The
ds.diff_dir variable has been introduced to point to the correct data directory.

More fixes for the Structure.test_create_diff_tensor_pdb_oblate system test.

The initial Diso value is now set to the real final Diso, and the PDB file contents have been
updated for the fixed oblate spheroidal diffusion relaxation data.

Fix for the oblate spheroid diffusion relaxation data.

The diffusion parameters are constrained as Dx <= Dy <= Dz.

Copyright update.

The Structure.test_create_diff_tensor_pdb_oblate now uses oblate diffusion relaxation data.

This fixes bug #23232 (https://gna.org/bugs/?23232), the failure of this system test on Mac OS X.
The problem was that the system test was previously using relaxation data for prolate spheroidal
diffusion and fitting an oblate tensor to that data. This caused the solution to be slightly
different on different CPUs, operating systems, Python versions, etc. and hence the PDB file
representation of the diffusion would be slightly different.

Creation of oblate spheroid diffusion relaxation data.

This will be used in the Structure.test_create_diff_tensor_pdb_oblate system test.

Test data directory renaming.

The test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed to spheroid_prolate.
This is in preparation for creating oblate spheroid diffusion relaxation data.

Fix for the internal structural object atomic coordinate assembly function.

This is the pipe_control.structure.main.assemble_structural_coordinates() function. The case of no
sequence alignment being required as only models are being handled is now functional. The strings
and gaps data structures passed into the lib.sequence_alignment.msa.msa_residue_skipping() function
for generating the residue skipping data structure are now set to the one letter codes and an empty
structure of zeros respectively.

Fix for the lib.sequence_alignment.msa.msa_residue_skipping() function.

The sequences argument for passing in the one letter codes has been removed. The per molecule loop
should be over the alignment strings rather than one letter codes, otherwise the loop will be too
short.

The structure.sequence_alignment user function now sets some arguments to None before storage.

This is for all arguments not used in the sequence alignment. For example the residue number based
alignment does not use the gap penalties, pairwise alignment algorithm or the substitution matrices.