relax SVN archive

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'Order parameters' has been replaced by 'Cone half angles' to clarify what the values really are.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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Merged revisions 26069-26070 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26069 | bugman | 2014-09-26 18:19:27 +0200 (Fri, 26 Sep 2014) | 5 lines

Added checks to the Bmrb.test_bug_22704_corrupted_state_file system test.

This is to see if the cdp.exp_info data structure has been correctly restored from the save file.
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r26070 | bugman | 2014-09-26 18:24:44 +0200 (Fri, 26 Sep 2014) | 3 lines

Uncommented some checks in the Bmrb.test_bug_22704_corrupted_state_file system test.
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Merged revisions 26067-26068 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26067 | bugman | 2014-09-26 17:34:15 +0200 (Fri, 26 Sep 2014) | 11 lines

Fix for the experimental information data pipe object when converting to XML state and results files.

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 names and descriptions for the software, citation and script list objects were incorrectly set.
These have been fixed so that the name of the data structure and the real description is present in
the XML state or results file instead of <relax_list desc='relax list container'>.
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r26068 | bugman | 2014-09-26 17:44:48 +0200 (Fri, 26 Sep 2014) | 11 lines

Fix for the experimental information data pipe object when converting to XML state and results files.

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 names and descriptions for the software, citation and script list objects were incorrectly set.
These have been fixed so that the name of the data structure and the real description is present in
the XML state or results file instead of <relax_list desc='relax list container'>.
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Merged revisions 26065-26066 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26065 | tlinnet | 2014-09-26 17:29:39 +0200 (Fri, 26 Sep 2014) | 3 lines

Implemented getting the statistics for parameters and comparing to init NI.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r26066 | tlinnet | 2014-09-26 17:29:49 +0200 (Fri, 26 Sep 2014) | 3 lines

Implemented writing and plotting of statistics for individual and clustered fitting, compararing to full NI.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 26064 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26064 | bugman | 2014-09-26 16:46:20 +0200 (Fri, 26 Sep 2014) | 3 lines

Removed a debugging printout fatal for Python 3.
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Merged revisions 26063 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26063 | bugman | 2014-09-26 16:36:13 +0200 (Fri, 26 Sep 2014) | 6 lines

Created the Bmrb.test_bug_22704_corrupted_state_file system test.

This is to catch 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.
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Merged revisions 26058-26062 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26058 | bugman | 2014-09-26 14:38:48 +0200 (Fri, 26 Sep 2014) | 6 lines

Fixes for the lib.checks.Check object.

The __call__() method keyword arguments **kargs needs to be processed inside the method to strip out
the escalate argument.
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r26059 | bugman | 2014-09-26 14:45:05 +0200 (Fri, 26 Sep 2014) | 5 lines

The default value of the escalate argument of the Check.__call__() method is now 2.

This will cause the calls to the check_*() function/objects to default to raising RelaxErrors.
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r26060 | bugman | 2014-09-26 15:06:55 +0200 (Fri, 26 Sep 2014) | 16 lines

Reverted r26053, as this is no longer the case.

The command used was:
svn merge -r26053:r26052 .

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r26053 | bugman | 2014-09-26 11:44:00 +0200 (Fri, 26 Sep 2014) | 5 lines
Changed paths:
M /trunk/test_suite/system_tests/bmrb.py

Updated the Bmrb.test_bug_22703_display_empty system/GUI test.

The RelaxError type is now different.
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r26061 | bugman | 2014-09-26 15:17:39 +0200 (Fri, 26 Sep 2014) | 6 lines

Changed the behaviour of the lib.checks.Check object again.

This time the registered function is stored rather than converted into a class instance method.
That way the check_*() function-like objects do not need to accept the unused 'self' argument.
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r26062 | bugman | 2014-09-26 15:29:07 +0200 (Fri, 26 Sep 2014) | 5 lines

The data pipe testing function has been converted to the strategy design pattern of the Check object.

The function pipe_control.pipes.test() has also been renamed to check_pipe().
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