relax SVN archive

Improvements for PDB creation in the relax library for out of bounds structural coordinates.

The lib.structure.pdb_write module atom() and hetatm() functions will now more gracefully handle
atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999]. When such
coordinates are encountered, instead of producing a too long PDB line which does not pass the
validation step, the functions will set the coordinates to the boundary value. This will at least
allow a valid PDB file to be created, despite the warping of the coordinates.

Merged revisions 26198-26200 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26198 | tlinnet | 2014-10-07 21:35:05 +0200 (Tue, 07 Oct 2014) | 1 line

Changed bounds for sample scripts to create: 3D iso-surface plot, surface plot and simulation of dispersion curves.
........
r26199 | tlinnet | 2014-10-07 21:35:08 +0200 (Tue, 07 Oct 2014) | 3 lines

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

Also added the new data for the plotting.
........
r26200 | tlinnet | 2014-10-07 21:35:11 +0200 (Tue, 07 Oct 2014) | 1 line

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

Merged revisions 26197 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26197 | tlinnet | 2014-10-07 21:35:03 +0200 (Tue, 07 Oct 2014) | 6 lines

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.
........

Merged revisions 26189-26196 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26189 | tlinnet | 2014-10-07 15:45:35 +0200 (Tue, 07 Oct 2014) | 3 lines

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
........
r26190 | bugman | 2014-10-07 16:11:38 +0200 (Tue, 07 Oct 2014) | 10 lines

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.
........
r26191 | bugman | 2014-10-07 16:21:30 +0200 (Tue, 07 Oct 2014) | 8 lines

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.
........
r26192 | bugman | 2014-10-07 16:31:49 +0200 (Tue, 07 Oct 2014) | 6 lines

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.
........
r26193 | bugman | 2014-10-07 16:44:32 +0200 (Tue, 07 Oct 2014) | 7 lines

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.
........
r26194 | bugman | 2014-10-07 17:45:07 +0200 (Tue, 07 Oct 2014) | 9 lines

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.
........
r26195 | bugman | 2014-10-07 17:47:01 +0200 (Tue, 07 Oct 2014) | 6 lines

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.
........
r26196 | tlinnet | 2014-10-07 18:43:52 +0200 (Tue, 07 Oct 2014) | 26 lines

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
........

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

........
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.
........

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