relax SVN archive

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.

Merged revisions 22530-22533 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22530 | bugman | 2014-03-26 15:57:21 +0100 (Wed, 26 Mar 2014) | 9 lines

Improvements for the log converter script.

This is for the scripted used to convert SVN messages into a format for the relax release
announcement.

The script now handles spacing better. Multi-line messages are now concatenated into a single line
using a double space between separate sentences and a single space in all other cases.
........
r22531 | bugman | 2014-03-26 16:14:18 +0100 (Wed, 26 Mar 2014) | 7 lines

Improvements for the pipe_control.mol_res_spin.generate_spin_id_unique() function.

The unique spin ID now takes into account if the molecule is named or not (for single molecules).
This allows the function to be used when dealing with the structural data rather than the molecule,
residue, and spin data structure.
........
r22532 | bugman | 2014-03-26 16:20:58 +0100 (Wed, 26 Mar 2014) | 3 lines

Copyright update.
........
r22533 | bugman | 2014-03-26 16:22:18 +0100 (Wed, 26 Mar 2014) | 6 lines

Removed the full stop from the printout of the test names in the test suite.

This allows for quicker copying and pasting of the test name when running with the --time option and
then selecting a single test to run.
........

Removed the full stop from the printout of the test names in the test suite.

This allows for quicker copying and pasting of the test name when running with the --time option and
then selecting a single test to run.

Copyright update.

Improvements for the pipe_control.mol_res_spin.generate_spin_id_unique() function.

The unique spin ID now takes into account if the molecule is named or not (for single molecules).
This allows the function to be used when dealing with the structural data rather than the molecule,
residue, and spin data structure.

Improvements for the log converter script.

This is for the scripted used to convert SVN messages into a format for the relax release
announcement.

The script now handles spacing better. Multi-line messages are now concatenated into a single line
using a double space between separate sentences and a single space in all other cases.

Shifted all of the code for calculating the frame order rotor axis into lib.frame_order.rotor_axis.

The new frame_order.rotor_axis module consists of three function for creating a unit vector or the
rotor axis using either the axis alpha angle, the two spherical angles or the three Euler angles.

Updated the chi2 value check in some of the CaM frame order system tests for the rotor model.

The chi2 value is slightly different due to truncation and conversion artifacts of the parameter set
reduction.