relax SVN archive

Modified the printouts for the unit tests when running with the --time command line option.

The test name is now being processed. The leading 'test_suite.unit_tests.' text is now stripped
out. And the remaining text is split into the module name and the test name. This is to allow the
unit test module name to be more easily identifiable, so it can then be used as a command line
option to allow only a subset of tests to be performed.

Big improvement for running the relax unit tests via the relax command line options.

The unit test module path is now accepted as a command line option. This brings more capabilities
of Gary Thompson's test_suite/unit_tests/unit_test_runner.py script into the relax command line.
The _pipe_control/test_value unit test module path can be specified as, for example, one of
'test_suite.unit_tests._pipe_control.test_value', 'test_suite/unit_tests/_pipe_control/test_value',
'_pipe_control.test_value', '_pipe_control/test_value'. This allows individual modules of tests to
be run, rather than having to execute all unit tests, which is very useful for debugging.

Added some test pymol script, to create dx maps and chi2 surface plot.

These will go to the wiki: http://wiki.nmr-relax.com/Chi2_surface_plot

Epydoc change for DOI reference in systemtests.

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

Merged revisions 26176 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26176 | bugman | 2014-10-06 18:20:25 +0200 (Mon, 06 Oct 2014) | 7 lines

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.
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Merged revisions 26175 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26175 | tlinnet | 2014-10-06 18:11:05 +0200 (Mon, 06 Oct 2014) | 1 line

Fix for epydoc in systemtest Relax_disp.test_dx_map_clustered.
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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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