relax SVN archive

Changed the Noe analysis sample script to properly handle the peak intensity Grace plots.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot. These
changes match those of the test suite.

Changed the Noe.test_noe_analysis system test to handle the peak intensities correctly.

This relates to bug #21863 (https://gna.org/bugs/?21863), , the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot.

Merged revisions 22541 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22541 | bugman | 2014-03-26 18:20:40 +0100 (Wed, 26 Mar 2014) | 10 lines

Fix for the NOE analysis for the peak intensity parameters.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

The 'ref' and 'sat' parameters have been replaced by the 'intensities' dictionary data structure a
long, long time ago. Therefore they have been eliminated and replaced by the 'intensities'
definition.
........

Fix for the NOE analysis for the peak intensity parameters.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

The 'ref' and 'sat' parameters have been replaced by the 'intensities' dictionary data structure a
long, long time ago. Therefore they have been eliminated and replaced by the 'intensities'
definition.

Merged revisions 22539 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22539 | bugman | 2014-03-26 17:59:15 +0100 (Wed, 26 Mar 2014) | 7 lines

Improved the user feedback when executing a user function in the GUI.

The busy cursor is now turned on at the start of the user function wizard page method _apply() and
turned off again at the end. This would avoid user confusion, thinking that the program has frozen
(as was the case in bug #21862, https://gna.org/bugs/?21862).
........

Improved the user feedback when executing a user function in the GUI.

The busy cursor is now turned on at the start of the user function wizard page method _apply() and
turned off again at the end. This would avoid user confusion, thinking that the program has frozen
(as was the case in bug #21862, https://gna.org/bugs/?21862).

Merged revisions 22537 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22537 | bugman | 2014-03-26 17:43:37 +0100 (Wed, 26 Mar 2014) | 5 lines

Modified the Noe.test_noe_analysis system test to catch bug #21863 (https://gna.org/bugs/?21863).

This is the failure to create the ref and sat Grace 2D plots in the NOE analysis.
........

Modified the Noe.test_noe_analysis system test to catch bug #21863 (https://gna.org/bugs/?21863).

This is the failure to create the ref and sat Grace 2D plots in the NOE analysis.

Merged revisions 22535 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22535 | bugman | 2014-03-26 17:28:19 +0100 (Wed, 26 Mar 2014) | 13 lines

Huge speed up of the interatom.define user function.

This is to fix bug #21862 (https://gna.org/bugs/?21862), the freezing up of relax when using the dipolar relaxation button in the model-free auto-analysis in the GUI.

This involves a number of changes. The algorithm for the backend of the interatom.define user function has been broken into two separate parts. The first part is new and uses the internal structural object atom_loop() twice for each spin ID string. This then calls the new are_bonded_index() structural object method which uses atom indices to find if two atoms are bonded, as the atom indices are returned from the atom_loop(). The are_bonded_index() is orders of magnitude faster than are_bonded() as selection objects are not used and the bonded data structure can be directly accessed. The are_bonded() method has also been slightly speed up by improving its logic.

The second part is to perform the original algorithm of two nested spin loops over each spin ID and using the are_bonded() structural method. This second part only happens if the first part finds nothing.

The structural object atom_loop() method has been modified to be able to return the molecule index. These indices are needed for the new are_bonded_index() method.

When running relax with the profile flag turned on, a simple script which loads the 'Ubiquitin2.bz2' saved state and then the "interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)" user function decreases from a total time of 143 to 3.8 seconds. However there are no speed changes detectable in the relax test suite - on one computer the system, unit and GUI tests only only vary by a fraction of a second.
........

Huge speed up of the interatom.define user function.

This is to fix bug #21862 (https://gna.org/bugs/?21862), the freezing up of relax when using the dipolar relaxation button in the model-free auto-analysis in the GUI.

This involves a number of changes. The algorithm for the backend of the interatom.define user function has been broken into two separate parts. The first part is new and uses the internal structural object atom_loop() twice for each spin ID string. This then calls the new are_bonded_index() structural object method which uses atom indices to find if two atoms are bonded, as the atom indices are returned from the atom_loop(). The are_bonded_index() is orders of magnitude faster than are_bonded() as selection objects are not used and the bonded data structure can be directly accessed. The are_bonded() method has also been slightly speed up by improving its logic.

The second part is to perform the original algorithm of two nested spin loops over each spin ID and using the are_bonded() structural method. This second part only happens if the first part finds nothing.

The structural object atom_loop() method has been modified to be able to return the molecule index. These indices are needed for the new are_bonded_index() method.

When running relax with the profile flag turned on, a simple script which loads the 'Ubiquitin2.bz2' saved state and then the "interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)" user function decreases from a total time of 143 to 3.8 seconds. However there are no speed changes detectable in the relax test suite - on one computer the system, unit and GUI tests only only vary by a fraction of a second.