relax SVN archive

Fixes and simplifications for the pipe_control.pipes.check_pipe() checking object.

One of the RelaxError classes were not initialised and the docstring was incorrect.

Implemented the structure.mean user function frontend.

The backend is currently just a stub function.

Created the Structure.test_mean system test.

This is to test the functionality of a planned new feature, the structure.mean user function. This
is an analysis aid that will calculate the mean structure from all loaded models.

Implemented counting of outliers for statistics.

This is to get a better feeling why some statistics are very much different between NI.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Improvements to the summary table for the frame order auto-analysis.

The rotor and free rotor model motional eigenframe parameter axis_alpha is now being converted into
spherical angles and reported in the table. This allows the motional eigenframe of all models to be
easily compared in the table.

Merged revisions 26085,26087-26088 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26085 | tlinnet | 2014-09-27 12:20:33 +0200 (Sat, 27 Sep 2014) | 12 lines

For relaxation dispersion, modified that the Grid search and linear constraints for parameter "k_AB" is between 0-100.

The parameter is only used in the TSMFK01 model.

The "k_AB" parameter is only for very slow forward exchange rate.
The extected values should according to the reference paper:

Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., and Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an sh3 domain. J. Am. Chem. Soc., 123(46), 11341-11352. (10.1021/ja011300z)

The paper conserns values of k_AB in the region 0.1 to 5.0.

If the exchange rate is any higher value of this, then another model should be used for the analysis.
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r26087 | tlinnet | 2014-09-27 14:49:46 +0200 (Sat, 27 Sep 2014) | 3 lines

Set the default insignificance value to 0.0 instead of 1.0.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r26088 | tlinnet | 2014-09-27 16:33:01 +0200 (Sat, 27 Sep 2014) | 3 lines

Modified the Grid search limits for parameter "k_AB" to be between 0.1 and 20.0 rad/s.

This is for the TSMFK01 model, where values much above 10/20 is not expected.
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Possible fixes for the frame order auto-analysis.

This is just in case a user decides to not perform the optimisation starting with a PCS subset. In
this case, the analysis will now execute correctly.

Improvements for the sectioning printouts for the frame order auto-analysis.

The sections now use the lib.text.formatting subtitle() and subsubtitle() functions to distinguish
them from the output of all the user functions, which use the section(), subsection() and
subsubsection() functions. New sectioning printouts have been added for clarity.

Improvements, fixes, and expansion of the results and data visualisation file creation.

This is for the frame order auto-analysis. The visualisation() method has been renamed to
results_output() and its scope expanded. The function previously only called the
frame_order.pdb_model and frame_order.simulation user functions for creating PDB representations of
the frame order motions and performing a pseudo-Brownian frame order dynamics simulate. This has
been extended to also call the results.write user function for outputting results files and the
rdc.corr_plot and pcs_corr_plot for generating correlation plots of the measured vs. back-calculated
data.

All parts of the auto-analysis were output files are required now call this method. This ensures
that all output files are always created, and are placed into the correct directories.

Removed the call to the frame_order.simulate user function for the rigid model in the auto-analysis.

There is no motion to simulate in the rigid model, so the frame_order.simulate user function has no
use.