relax SVN archive

Added the displace_id argument to the structure.align and structure.superimpose user functions.

This gives both of these user functions finer control over which atoms are translated and rotated by
the algorithm. This allows, for example, to align structures based on a set of backbone heavy atoms
while the protons and side chains are displaced by default. Or if a domain is aligned, then just
that domain can be displaced.

Modified some system tests of the structure.align and structure.superimpose user functions.

The displace_id argument has been introduced for both of these user functions for finer control over
which atoms are translated and rotated by the algorithm. This allows, for example, to align
structures based on a set of backbone heavy atoms while the protons and side chains are displaced by
default. Or if a domain is aligned, then just that domain can be displaced.

Modified the Structure.test_superimpose_fit_to_mean system test.

This is also to demonstrate a bug, this time in the structure.superimpose user function, in which
the algorithm causes a translation and rotation of all atoms rather than just those selected by the
atom_id argument.

Modified the Structure.test_align system test to show a failure of the structure.align user function.

The alignment causes all atoms in the structural object to be translated and rotated, whereas it
should only operate on the atoms of the atom_id argument.

Removed a debugging printout.

Fix for the Structure.test_displacement system test for the assemble_coord_array() function bugfix.

Fix for the IDs returned by lib.structure.internal.coordinates.assemble_coord_array().

The list of unique structure IDs was being incorrectly constructed if multiple molecules are present
but the molecules argument was not supplied. It would be of a different size to the coordinate data
structure.

Converted the structure.web_of_motion user function to the new pipe/model/molecule/atom_id design.

This allows the web of motion representation to work on atomic coordinates from different data
pipes, different structural models, and different molecules. The user function backend uses the new
pipe_control.structure.main.assemble_coordinates() function to assemble the common atom coordinates,
molecule names, residue names, residue numbers, atom names and elements. All this information is
then used to construct the new web of motion PDB file. Therefore the entire backend has been
rewritten.

The Structure.test_web_of_motion_12, Structure.test_web_of_motion_13, and
Structure.test_web_of_motion_all system tests have all been updated for the changed
structure.web_of_motion user function arguments. In addition, the system tests
Structure.test_web_of_motion_12_molecules, Structure.test_web_of_motion_13_molecules and
Structure.test_web_of_motion_all_molecules have been created as a copy of the other tests but with
the 3 structures loaded as different molecules.

Bug fix for the lib.arg_check.is_int_list() function for checking a list of lists.

This is used to check user function arguments, but was causing a RelaxError to be raised for all
integer list of lists user function arguments when a valid value is supplied. The function has been
updated to match the is_str_list() function which does not suffer from this bug.

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

The pipes list was no longer being created as it was shifted to the assemble_coordinates() function,
however it is required for the translation and rotation function calls.