relax SVN archive

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.

Removed some temporary printouts from the structure.align user function.

Implemented the new molecules argument for the structure.rmsd user function.

This allows the RMSD between different molecules rather than different models to be calculated,
extending the functionality of this user function.

Created the Structure.test_rmsd_molecules system test.

This will be used to implement a new molecules argument for the structure.rmsd user function so that
the RMSD between different molecules rather than different models can be calculated.