relax SVN archive

Merged revisions 26188 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26188 | tlinnet | 2014-10-07 15:45:32 +0200 (Tue, 07 Oct 2014) | 3 lines

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.
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Modified the example data, after issue with parameters was fixed.

Minor changes to python matplotlib script, to produce surface plot.

Also added the new data for the plotting.

Changed bounds for sample scripts to create: 3D iso-surface plot, surface plot and simulation of dispersion curves.

Critical fix, for k_AB not belonging to list of global parameters.

k_AB was only changed to the spin of interest, but not for the rest of the cluster.
When the parameter vector is assembled, "assemble_param_vector(spins=spins)" it takes the global parameter from spin 0.

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

Added script to simulate dispersion profiles at different settings.

This shows that something is wrong.

The back-calculated values in the graphs are not equal to the interpolated values.
There must be something wrong somewhere.

This list shows the chi2 values, and judging from the dispersion graphs, this simply cannot be True.

10.405 2.414 6722.833
9.900 1.000 6722.159
9.900 2.333 6722.159
9.900 3.667 6722.159
9.900 5.000 6722.159
10.300 1.000 6722.156
10.300 2.333 6722.156
10.300 3.667 6722.156
10.300 5.000 6722.156
10.700 1.000 6726.040
10.700 2.333 6726.040
10.700 3.667 6726.040
10.700 5.000 6726.040
11.100 1.000 6732.256
11.100 2.333 6732.256
11.100 3.667 6732.256
11.100 5.000 6732.256

Removal of repetitive code in the relaxation dispersion model_loop() API method.

The spin loop does not need to be called twice, instead the if statements have been modified to
better direct the code execution.

Fix for the Test_value.test_value_set_r1_rit test of the _pipe_control.test_value unit test module.

This is a general fix for all unit test modules which use the
test_suite.unit_tests.value_testing_base.Value_testing_base base class. After the molecules,
residues and spins are manually created, the pipe_control.mol_res_spin.metadata_update() function is
called to make sure that all of the private and volatile metadata have been correctly created, so
that the other pipe_control.mol_res_spin module functions can operate correctly.

Fix for the Bmrb.test_bug_22704_corrupted_state_file GUI test.

This was failing because the setUp() method in the inherited Bmrb system test module was being
overwritten by the default Unittest.setUp() method. Therefore the system test setUp() method has
been copied into the GUI test class.

Modified the help strings for the test suite options shown when 'relax -h' is run.

The ability to specify individual tests (or modules of tests for the unit tests) is now documented.
The '--time' option help string has also been edited.