relax SVN archive

Expanded the Structure.test_delete_atom system test.

This is to show that the structure.write_pdb user function fails after a call to the
structure.delete user function to delete individual atoms.

Created the Structure.test_delete_atom system test.

This is used to test the deletion of a single atom using the structure.delete user function.

Bug fix for the structure.delete user function.

When individual atoms are deleted, the bonded atom data structure is no correctly updated to remove
the now non-existent atom.

Modified the Structure.test_align system test to call the structure.write_pdb user function.

This sets the file name to sys.stdout so that the original structure and the final aligned
structures are output to STDOUT for debugging purposes.

Small whitespace fix.

The pipe_control.structure.main.check_structure() checking object now accepts the pipe_name argument.

This allows structural data to be checked for in different data pipes without having to switch to
them.

The pipe_control.structure.main functions translate() and rotate() now accept the pipe_name argument.

This is used to translate and rotate structures in different data pipes, as required by the
structure.align user function.

Implemented the structure.align user function backend.

This is similar to the structure.superimpose user function, however the coordinate data structure
only contains atoms which are in common to all structures.

Modified the Structure.test_align system test so that translations and rotations match the algorithm.

This allows the output of the structure.align user function to be checked to see if the rotation
matrix and translation vector found match that used to shift the original structures.

Extended the Structure.test_align system test to throughly check the structural data.

This includes changing the structure.align user function call to use 'fit to first' and carefully
checking the new atomic coordinates.