relax SVN archive

Updates for the structure.sequence_alignment user function.

This is for the changes to the lib.structure.internal.coordinates.assemble_atomic_coordinates()
function return values. The new object ID, model, and molecule flat lists are used directly for
storing the alignment results in the relax data store.

Modified the data returned by lib.structure.internal.coordinates.assemble_atomic_coordinates().

The function will now assemble simple lists of object IDs, model numbers and molecule names with
each list element corresponding to a different structural model. This will be very useful for
converting from the complicated pipes, models, and molecules user function arguments into relax data
store independent flat lists.

Implemented the data store Sequence_alignments.from_xml() method.

This method is required for being able to read RelaxListType objects from the XML file.

Fixes for handling the sequence_alignments data store object.

More advanced support for different numpy number types in the lib.xml relax library module.

This allows numpy int16, int32, float32, and float64 objects to be stored and retrieved from relax
XML save and results files.

Fix for a fatal bug introduced in the last commit (r27398).

The data store ds.sequence_alignment object is now being treated as special and is blacklisted.

The object is now explicitly recreated in the data store from_xml() method.

Fixes for the sequence alignment objects for the relax data store.

The Sequence_alignments(RelaxListType) and Alignment(Element) classes were not being set up
correctly. The container names and descriptions were missing.

Implemented the backend of the structure.sequence_alignment user function.

This checks some of the input parameters, assembles the structural objects then the atomic
coordinate information, performs the multiple sequence alignment, and then stores the results.

Spun out the atomic assembly code of the assemble_coord_array() function.

The code from the lib.structure.internal.coordinates.assemble_coord_array() function has been
shifted to the new assemble_atomic_coordinates(). This is to simplify assemble_coord_array() as
well as to isolate the individual functionality for reuse.