relax SVN archive

Fix for the new pipe_control.structure.main.assemble_structural_coordinates() function.

The atom_id argument is now passed into the assemble_atomic_coordinates() function of the
lib.structure.internal.coordinates module so that atom subsets are once again recognised.

Fix for the structure.superimpose user function if no data pipes are supplied.

This reintroduces the pipes list construction.

Updated the structure.web_of_motion 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.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.