relax SVN archive

Merged revisions 26167-26174 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26167 | tlinnet | 2014-10-06 17:07:49 +0200 (Mon, 06 Oct 2014) | 3 lines

In the dispersion API calculate(), used the API function model_loop() to loop over the clusters instead.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26168 | tlinnet | 2014-10-06 17:07:54 +0200 (Mon, 06 Oct 2014) | 5 lines

Removed then function loop_cluster_ids() from dispersion API().

This should be implemented elsewhere.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26169 | tlinnet | 2014-10-06 17:07:55 +0200 (Mon, 06 Oct 2014) | 3 lines

Updated the API set_param_values() function to use model_loop() to get the spin_ids from the cluster.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26170 | tlinnet | 2014-10-06 17:07:57 +0200 (Mon, 06 Oct 2014) | 11 lines

Initial try to fix unit test test_value_set_r1_rit().

The problem is, that no spin-id can be generated, since the spins are created manually,

"
File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/pipe_control/mol_res_spin.py", line 1498, in generate_spin_id_unique
if res and res.name != None and mol._res_name_count[res.name] > 1:
AttributeError: 'MoleculeContainer' object has no attribute '_res_name_count'
"

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26171 | tlinnet | 2014-10-06 17:21:32 +0200 (Mon, 06 Oct 2014) | 3 lines

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.
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r26172 | tlinnet | 2014-10-06 18:03:28 +0200 (Mon, 06 Oct 2014) | 3 lines

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.
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r26173 | tlinnet | 2014-10-06 18:03:30 +0200 (Mon, 06 Oct 2014) | 3 lines

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.
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r26174 | tlinnet | 2014-10-06 18:03:32 +0200 (Mon, 06 Oct 2014) | 10 lines

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.
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Merged revisions 26165-26166 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26165 | bugman | 2014-10-06 16:35:18 +0200 (Mon, 06 Oct 2014) | 7 lines

Fix for the pipe_control.exp_info.bmrb_write_software() function.

This was broken back at r26071 (http://article.gmane.org/gmane.science.nmr.relax.scm/23822). The
variable name change of software.name to software.software_name was not applied to the
pipe_control.exp_info module. This caused a few of the Bmrb system tests to fail.
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r26166 | bugman | 2014-10-06 16:37:17 +0200 (Mon, 06 Oct 2014) | 5 lines

Added a BMRB NMR-STAR formatted deposition file for the OMP model-free data for reference.

This is because there are no other NMR-STAR formatted files in the relax sources.
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Merged revisions 26164 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26164 | bugman | 2014-10-06 14:38:25 +0200 (Mon, 06 Oct 2014) | 7 lines

Fix for bug #22563 (https://gna.org/bugs/?22563).

This is the NS MMQ 2-site dispersion model running at 32-bit precision and not 64-bit as it should
be. The numpy.complex64 32-bit types have been replaced by numpy.complex128 in the
lib.dispersion.ns_mmq_2site module.
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Merged revisions 26151-26163 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26151 | tlinnet | 2014-10-06 02:39:43 +0200 (Mon, 06 Oct 2014) | 3 lines

Inserted a check in systemtest Relax_disp.test_dx_map_clustered, that a call to minimise.calculate() should be the same as the file stored with the clustered chi2 value.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26152 | tlinnet | 2014-10-06 02:39:46 +0200 (Mon, 06 Oct 2014) | 3 lines

Made initial preparation to loop over clustered spins and ids for minimise.calculate() call.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26153 | tlinnet | 2014-10-06 02:39:48 +0200 (Mon, 06 Oct 2014) | 3 lines

Implemented looping over spin-clusters when issuing a minimise.calculate().

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26154 | tlinnet | 2014-10-06 02:39:50 +0200 (Mon, 06 Oct 2014) | 3 lines

Made back_calc_r2eff() in optimisation module use the spin and id list instead.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26155 | tlinnet | 2014-10-06 02:39:51 +0200 (Mon, 06 Oct 2014) | 3 lines

Fix for graph plotting functionality to send spins as list of one spins.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26156 | tlinnet | 2014-10-06 02:39:53 +0200 (Mon, 06 Oct 2014) | 3 lines

Fix for calling back_calc_r2eff with the new argument keywords, and use list of spin and spind ids.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26157 | tlinnet | 2014-10-06 02:39:55 +0200 (Mon, 06 Oct 2014) | 3 lines

Fix for synthetic script calling back_calc_r2eff() with old arguments and to use list of spin containers and ids.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26158 | tlinnet | 2014-10-06 02:45:16 +0200 (Mon, 06 Oct 2014) | 3 lines

Inserted last test in test_dx_map_clustered, to check out the written chi2 values are as expected.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26159 | tlinnet | 2014-10-06 05:19:08 +0200 (Mon, 06 Oct 2014) | 3 lines

Moved the looping over cluster spin ids into its own function in the API.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26160 | tlinnet | 2014-10-06 05:19:11 +0200 (Mon, 06 Oct 2014) | 3 lines

Added the selection string for all the cluster ids to be parsed back as well.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26161 | tlinnet | 2014-10-06 05:19:13 +0200 (Mon, 06 Oct 2014) | 3 lines

Made the value set function, set values to all spins, if it is a global parameter.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26162 | tlinnet | 2014-10-06 05:19:15 +0200 (Mon, 06 Oct 2014) | 3 lines

Moved teh skipping of protons away from looping function.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26163 | tlinnet | 2014-10-06 05:50:02 +0200 (Mon, 06 Oct 2014) | 7 lines

Inserted some testing lines for making a dx_map, either global clustered or as a free spin.

There is a big difference which dx map you get.

It illustrates beautiful, the effect of clustering things together.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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Merged revisions 26149-26150 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26149 | tlinnet | 2014-10-05 22:22:35 +0200 (Sun, 05 Oct 2014) | 3 lines

Implemented systemtest Relax_disp.test_dx_map_clustered to cath the missing creation of a point file.

Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work when only 1 point is used.
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r26150 | tlinnet | 2014-10-05 22:22:38 +0200 (Sun, 05 Oct 2014) | 5 lines

Fix for writing out point files, when only one point is used.

The code was testing for > 1 points to be present, before writing out point files.

Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work when only 1 point is used.
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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.