relax SVN archive

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.

Creation of the lib.sequence_alignment.msa.msa_general() function.

This consists of code from the structure.sequence_alignment user function backend function
pipe_control.structure.main.sequence_alignment() for selecting between the different sequence
alignment methods.

Updated the Structure.test_align_CaM_BLOSUM62 system test script.

The MSA algorithm and pairwise alignment algorithms are now specified in the
structure.sequence_alignment user function calls.

Modified the structure.sequence_alignment user function arguments.

The pairwise_algorithm and matrix arguments can no be None, and they default to None.

Corrections and simplifications for the Structure.test_sequence_alignment_residue_number system test.

Created the Structure.test_sequence_alignment_residue_number system test.

This will be used to test the structure.sequence_alignment user function together with the 'residue
number' MSA algorithm. This is simply a copy of the
Structure.test_sequence_alignment_central_star_nw70_blosum62 system test with a few small changes.

Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62 system test.

Some residues are now deleted so that the sequences are not identical.

Renamed the Structure.test_sequence_alignment_molecules system test.

The new name is Structure.test_sequence_alignment_central_star_nw70_blosum62, to better reflect what
the test is doing.