relax SVN archive

Merged revisions 26148 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26148 | tlinnet | 2014-10-03 18:34:35 +0200 (Fri, 03 Oct 2014) | 3 lines

Removed the showing of Matplotlib figures in the test suite.

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 26143-26147 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26143 | tlinnet | 2014-10-03 18:30:33 +0200 (Fri, 03 Oct 2014) | 8 lines

Added example CPMG data, which could possible be send for BMRB submission.

The data is un-published CPMG data, related to the paper:
- Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE
- Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
- (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI 10.1002/prot.22886

task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG experiments for BMRB
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r26144 | tlinnet | 2014-10-03 18:30:36 +0200 (Fri, 03 Oct 2014) | 3 lines

Added systemtest Relax_disp.test_bmrb_sub_cpmg() to try calling the bmrb functions in relax.

task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG experiments for BMRB
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r26145 | tlinnet | 2014-10-03 18:30:38 +0200 (Fri, 03 Oct 2014) | 3 lines

Implemented the initial part of the API, to collect data for BMRB submission.

task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG experiments for BMRB
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r26146 | tlinnet | 2014-10-03 18:30:40 +0200 (Fri, 03 Oct 2014) | 7 lines

Inserted a "RelaxImplementError" when trying to call bmrb_write from a relaxation dispersion analysis.

To implement the fucntion, it would require a re-write of the relax_data bmrb_write(star) function, and proper handling of cdp.ri_ids.
It was also not readily possible to find examples of submitted CPMG data in the BMRB database.
This makes it hard to develop, and even ensure that BMRB would accept the format.

task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG experiments for BMRB
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r26147 | tlinnet | 2014-10-03 18:30:41 +0200 (Fri, 03 Oct 2014) | 5 lines

Removed the systemtest Relax_disp.test_bmrb_sub_cpmg() to be tested in the test-suite.

This test will not be implemented, as it requires a large re-write of data structures.

task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG experiments for BMRB
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Merged revisions 26142 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26142 | tlinnet | 2014-10-02 21:55:58 +0200 (Thu, 02 Oct 2014) | 3 lines

Skippping of intensity calculation, if the intensity pipe does not exists.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Added 'relaxation dispersion' to the headers of the http://www.nmr-relax.com webpages.

These had not been updated since the relax_disp branch was merged into the relax trunk and relax
3.1.0 was released (http://wiki.nmr-relax.com/Relax_3.1.0). This should significantly help with
relax's search engine ranking when people search for 'relaxation dispersion' or related terms.

Updated all of the Relax_disp.test_korzhnev_2005_*_data system tests.

These now have slightly changed parameter values due to the fix of bug #22563
(https://gna.org/bugs/?22563), the NS MMQ 2-site dispersion model running at 32-bit precision and
not 64-bit as it should be.

Fix for epydoc in systemtest Relax_disp.test_dx_map_clustered.

Removed unused proton reference in relax_disp API calculate().

There is though some problems with these tests:
F 1.93 s for Relax_disp.test_korzhnev_2005_15n_dq_data
F 2.01 s for Relax_disp.test_korzhnev_2005_1h_mq_data
F 1.93 s for Relax_disp.test_korzhnev_2005_1h_sq_data

It is unsure where these comes from.

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

Fix for looping performed twice in relax_disp API model_loop().

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

Fix for references to "spin" in optimisation.back_calc_r2eff().

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

Removed the checking of MODEL_LIST_MMQ, and spin.isotope from optimisation.back_calc_r2eff(), since this check is already covered.

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