relax SVN archive

Updated the structure.rmsd user function for the changed atomic assembly logic.

This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main
module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or
the default of a residue number based alignment.

Updated the structure.atomic_fluctuations user function for the changed atomic assembly logic.

This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main
module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or
the default of a residue number based alignment.

Updated the structure.find_pivot user function for the changed atomic assembly logic.

This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main
module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or
the default of a residue number based alignment.

Updated the structure.displacement user function for the changed atomic assembly logic.

This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main
module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or
the default of a residue number based alignment.

Added a function for assemble the common atomic coordinates taking sequence alignments into account.

This is the new pipe_control.structure.main.assemble_structural_coordinates() function. It takes
the sequence alignment logic out of the lib.structure.internal.coordinates.assemble_coord_array()
function so that sequence alignments in the relax data store can be used. The logic has also been
redefined as: 1, use a sequence alignment from the relax data store if present; 2, use no sequence
alignment if coordinates only come from structural models; 3, fall back to a residue number based
alignment. The residue number based alignment is yet to be implemented.

As a consequence, the lib.structure.internal.coordinates.assemble_coord_array() function has been
greatly simplified. It no longer handles sequence alignments, but instead expects the residue
skipping data structure, built from the alignment, as an argument. The seq_info_flag argument has
also been eliminated in this function as well as the pipe_control.structure.main module.

Sequence alignments can now be retrieved without supplying the algorithm settings.

This is in the data_store.seq_align.Sequence_alignments.find_alignment() method. The change allows
for the retrieval of pre-existing sequence alignments at any stage.

Fix for the structure.sequence_alignment user function.

The alignment data should be stored in ds.sequence_alignments rather than ds.sequence_alignment.

Updated the Structure system tests for the structure.align and structure.superimpose user function merger.

Merger of the structure.align and structure.superimpose user functions.

The final user function is called structure.superimpose. As the sequence alignment component of the
structure.align user function has been shifted into the new structure.sequence_alignment user
function and the information is now stored in ds.sequence_alignments relax data store object, the
functionality of structure.align and structure.superimpose are now essentially the same. The
sequence alignment arguments and documentation has also been eliminated. And the documentation has
been updated to say that sequence alignments from structure.sequence_alignment will be used for
superimposing the structures.

Updates for the Structure.test_sequence_alignment_molecules system test.

This is required due to the changes in the backend of the structure.sequence_alignment user
function.