relax SVN archive

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.

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.

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.

Fix for the frame order optimisation target setup printouts.

The 'Numerical integration: ' printout was fixed to 'Quasi-random Sobol' sequence'. This now
changes to 'SciPy quadratic integration' if cdp.quad_int is set. The text 'PCS' has also been added
for clarification.

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.

Small change in the title of the summary table of the frame order auto-analysis.

'Order parameters' has been replaced by 'Cone half angles' to clarify what the values really are.

Fix for the change of the pipe_control.pipes.test() function to check_pipe().

Merged revisions 26071-26072 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26071 | bugman | 2014-09-26 18:29:26 +0200 (Fri, 26 Sep 2014) | 10 lines

Fix for the cdp.exp_info.software data structure setup.

This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files
after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user
functions.

The Element data container name was being replaced by the software name, making it impossible to
restore from the XML.
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r26072 | bugman | 2014-09-26 18:43:09 +0200 (Fri, 26 Sep 2014) | 10 lines

Implemented the cdp.exp_info.from_xml() method to correctly restore the experimental info structure.

This fixes bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting
the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions.

This custom ExpInfo.from_xml() method is required to properly recreate the software, script and
citation list data structures of the cdp.exp_info data structure, as these are special RelaxListType
objects populated by Element objects (both from data_store.data_classes).
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