relax SVN archive

Fixes for all the Ap4Aase truncated PDB files.

The atom numbers are now sequential, as defined by the PDB standard.

Fix for a copy and paste error in the Structure.test_read_merge system test.

Replaced many instances of the tab character '\t' with 4 spaces.

The MolList.add_item() structural API method now returns the added molecule container.

This is used by the pack_structs() method to alias the molecule, and will be required when structure
merging is implemented.

The merge flag for the structure.read_pdb user function is now propaged to the pack_structs() method.

This structure API method calls the ModelList.merge_item() method which is yet to be implemented.

Docstring fix for the structure.read_pdb user function backend.

Added the merge flag to the structure.read_pdb user function.

This currently does nothing.

Created the Structure.test_read_merge system test to test a new concept - merging of structures.

The idea is to add the merge argument to the structure.read_pdb user function to allow two different
structures in two PDB files to be merged. This is useful if structures of individual domains have
have been solved separately and are located in two PDB files. Then with the merge flag, you will
not need to use and external program or hand edit PDB files to join them.

Added a comment to the output from value.display and value.write to describe the parameter.

This idea is discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428.

The idea is to take the parameter description from the specific analysis API and add it to the top
of the file or output. This is to help understand what the Rex value are. For example for the Rex
parameter the first line would be:

# Parameter description: Chemical exchange relaxation (sigma_ex = Rex / omega**2).

Merged revisions 18839 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18839 | bugman | 2013-03-17 11:23:00 +0100 (Sun, 17 Mar 2013) | 6 lines

Backported the relax 2.2.4 CHANGES file to trunk.

The command used was:
svn merge -r18837:18838 svn+ssh://bugman@.../svn/relax/tags/2.2.4 .
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