relax SVN archive

Changes for water in the PDB file created by the structure.write_pdb user function.

The waters with the residue name 'HOH' are no longer output to HET records.

Fix for the displace_id and molecules arguments of the structure.align user function.

The atom ID used for the translations and rotations is now properly constructed from the molecule
names in the molecules list and the displace_id string.

Modified the Structure.test_align_molecules system test to catch a bug.

This is the failure of the displace_id argument of the structure.align user function when the
molecules argument is supplied - all atoms are being displaced instead of a subset.

Fixes for the Structure.test_superimpose_fit_to_mean system test for the displace_id argument.

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.