relax SVN archive

Implemented the multiple sequence alignment method based on residue numbers.

This is the new msa_residue_numbers() function in the lib.sequence_alignment.msa module. The logic
is rather basic in that the alignment is based on a residue number range from the lowest residue
number to the highest - i.e. it does not take into account gaps in common between all input
sequences.

Implemented the residue number based alignment in the atomic assembly function.

This is in the new pipe_control.structure.main.assemble_structural_coordinates() function. The code
for creating the residue skipping data structure is now shared between the three sequence alignment
options.

Another fix for the new pipe_control.structure.main.assemble_structural_coordinates() function.

The logic for determining if only models will be superimposed was incorrect.

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.