relax SVN archive

Bug fix for the CONECT records created by the structure.write_pdb user function.

The atom numbers inside the structural object were being used for the CONECT records rather than the
atom numbers used within the PDB file.

Another bug fix for the structure.delete user function when deleting individual atoms.

The bonded atom data structure consisting of indices requires all indices after the deleted atom to
be decremented by 1.

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.