relax SVN archive

Shift of the atomic coordinate assembly code into the relax library.

Most of the pipe_control.structure.main.assemble_coordinates() function has been shifted into the
assemble_coord_array() function of the new lib.structure.internal.coordinates module. The
pipe_control function now only checks the arguments and assembles the structural objects from the
relax data store, and then calls assemble_coord_array() to do all of the work.

This code abstraction increases the usefulness of the atomic coordinate assembly and allows it to be
significantly expanded in the future, for example by being able to take sequence alignments into
consideration.

Converted the structure.find_pivot user function to the new pipes/models/molecules/atom_id design.

This allows the motional pivot algorithm to work on atomic coordinates from different data pipes,
different structural models, and different molecules. The change allows the
Structure.test_find_pivot_molecules system test to now pass, as missing atomic data is now correctly
handled. The user function backend uses the new pipe_control.structure.main.assemble_coordinates()
function.

The Structure.test_find_pivot and Structure.test_find_pivot_molecules system tests have been updated
for the user function argument changes.

Changed the argument order for the structure.align user function.

The standardised order will now be pipes, models, molecules, atom_id, etc.

Shifted the atomic assembly code from the structure.align user function into its own function.

The new function assemble_coordinates() of the pipe_control.structure.main module will be used to
standardise the process of assembling atomic coordinates for all of the structure user functions.
This will improve the support for comparing different molecules rather than different models as
missing atoms or divergent primary sequence are properly handled, and it has multi-pipe support.

Implemented the molecules argument for the structure.find_pivot user function.

This allows the motional pivot optimisation between different molecules rather than different
models.

Increased the precision of pivot optimisation in the Structure.test_find_pivot_molecules system test.

Created the Structure.test_find_pivot_molecules system test.

This will be used to implement support for a molecules argument in the structure.find_pivot user
function so that different molecules rather than different models can be used in the analysis.

Created the Structure.test_find_pivot system test.

This is to check the structure.find_pivot user function as this algorithm is currently not being
checked in the test suite.

Implemented the molecules argument for the structure.displacement user function.

This allows the displacements (translations and rotations) to be calculated between different
molecules rather than different models. This information is stored in the dictionaries of the
cdp.structure.displacement object with the keys set to the molecule list indices.

Created the Structure.test_displacement_molecules system test.

This will be used to implement the new molecules argument for the structure.displacement user
function.