relax SVN archive

Updated the CHANGES document for relax 3.3.1.

Added the relax 3.3.1 manual to the repository.

Updated the version number to 3.3.1.

relax version 3.3.1.

This is a minor feature and bugfix release.

Expanded the list of global dispersion parameters in the set_param_values() API method.

This is a quick expansion of Troels' fix of r26197, to allow for the release of relax 3.3.1. This
is a small part of the discussion at
http://thread.gmane.org/gmane.science.nmr.relax.scm/23948/focus=7188.

Intermediate optimisation results are now stored by the frame order auto-analysis.

The results from each minimise.grid_search and minimise.execute user function call are now stored in
specially named directories located in the 'intermediate_results' directory, which itself is located
in the auto-analysis results_dir directory. This allows intermediate results to be more easily
analysed later on, which can be useful for optimising the optimisation steps. These directories can
also be used for the pre_run_dir auto-analysis argument for subsequent refinements from earlier
steps in the optimisation. The results stored include everything from the results_output() method
and the count_sobol_points() and summarise() functions.

To allow this to work, the auto-analysis functions count_sobol_points() and summarise() required
modification. Results files are now always loaded into a temporary data pipe, rather switching to
the corresponding pipe, and the temporary data pipe is deleted after the data has been extracted.
The original data pipe name is also stored and a switch back to that pipe occurs at the end of each
function.

Merged revisions 26205 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26205 | bugman | 2014-10-08 09:22:04 +0200 (Wed, 08 Oct 2014) | 9 lines

Improvements for PDB creation in the relax library for out of bounds structural coordinates.

The lib.structure.pdb_write module atom() and hetatm() functions will now more gracefully handle
atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999]. When such
coordinates are encountered, instead of producing a too long PDB line which does not pass the
validation step, the functions will set the coordinates to the boundary value. This will at least
allow a valid PDB file to be created, despite the warping of the coordinates.
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Improvements for PDB creation in the relax library for out of bounds structural coordinates.

The lib.structure.pdb_write module atom() and hetatm() functions will now more gracefully handle
atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999]. When such
coordinates are encountered, instead of producing a too long PDB line which does not pass the
validation step, the functions will set the coordinates to the boundary value. This will at least
allow a valid PDB file to be created, despite the warping of the coordinates.

Merged revisions 26198-26200 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26198 | tlinnet | 2014-10-07 21:35:05 +0200 (Tue, 07 Oct 2014) | 1 line

Changed bounds for sample scripts to create: 3D iso-surface plot, surface plot and simulation of dispersion curves.
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r26199 | tlinnet | 2014-10-07 21:35:08 +0200 (Tue, 07 Oct 2014) | 3 lines

Minor changes to python matplotlib script, to produce surface plot.

Also added the new data for the plotting.
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r26200 | tlinnet | 2014-10-07 21:35:11 +0200 (Tue, 07 Oct 2014) | 1 line

Modified the example data, after issue with parameters was fixed.
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Merged revisions 26197 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26197 | tlinnet | 2014-10-07 21:35:03 +0200 (Tue, 07 Oct 2014) | 6 lines

Critical fix, for k_AB not belonging to list of global parameters.

k_AB was only changed to the spin of interest, but not for the rest of the cluster.
When the parameter vector is assembled, "assemble_param_vector(spins=spins)" it takes the global parameter from spin 0.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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