relax SVN archive

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.

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

In addition to accepting the new argument, the user function backend has been redesigned for
flexibility. The assembly of coordinates and final rotations and translations now consist of three
loops over desired data pipes, all models, and all molecules. If the models or molecules arguments
are supplied, then the models or molecules in the loop which do not match are skipped. This logic
simplifies and cleans up the backend.

Change to the Structure.test_align system test.

The molecules argument for the structure.align user function has been changed to match the models
argument, in that it now needs to be a list of lists with the first dimension matching the pipes
argument. This change is to help with the implementation of the new structure.align functionality.

Some more fixes for the Structure.test_align_molecules system test.