relax SVN archive

Merged revisions 24841 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24841 | bugman | 2014-07-30 17:33:22 +0200 (Wed, 30 Jul 2014) | 6 lines

Grace string fixes for the alignment tensor parameters defined in the base parameter_object module.

This is essentially for allowing relax to run using Python 3. All Grace '\' characters need to be
escaped as '\\' in Python strings.
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Grace string fixes for the alignment tensor parameters defined in the base parameter_object module.

This is essentially for allowing relax to run using Python 3. All Grace '\' characters need to be
escaped as '\\' in Python strings.

Enabled pivot optimisation in the full_analysis.py script for the CaM frame order test data.

Fixes for the removal of the RDC data checks from the frame order optimisation functions.

The specific analysis API method overfit_deselect() has now been created to deselect spins which do
not have PCS data or interatomic data containers missing RDC data. The handling of deselected spins
and interatomic data containers is now also correctly handled throughout the frame order specific
code.

Merged revisions 24837 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24837 | bugman | 2014-07-30 17:01:58 +0200 (Wed, 30 Jul 2014) | 9 lines

Changed the behaviour of the pipe_control.structure.mass.pipe_centre_of_mass() function.

This function returns the CoM and optionally the mass of the structural data loaded into the current
data pipe. However it was matching the structural data to the molecule-residue-spin data structure
and skipping spins that were deselected. This illogical deselection part has been eliminated, as
spins can be deselected for various analysis purposes and this should not change the CoM. The
deletion also significantly speeds up the function.
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Changed the behaviour of the pipe_control.structure.mass.pipe_centre_of_mass() function.

This function returns the CoM and optionally the mass of the structural data loaded into the current
data pipe. However it was matching the structural data to the molecule-residue-spin data structure
and skipping spins that were deselected. This illogical deselection part has been eliminated, as
spins can be deselected for various analysis purposes and this should not change the CoM. The
deletion also significantly speeds up the function.

Removed the RDC data checks from the frame order optimisation.

This is in the minimise_setup_rdcs() and store_bc_data() functions of the
specific_analyses.frame_order.optimisation module, called before and after all optimisation. The
reason was identified by profiling - this check was adding significant amounts of time to the setup
and results unpacking parts of the optimisation. Specifically the interatomic_loop() function was
identified via profiling as the function requiring the most amount of cumulative time in the
Frame_order.test_auto_analysis system test (17 seconds out of a total of ~60 seconds).

Fix for the previous commit (r24834).

The results directory was incorrectly set.

Updated the full_analysis.py script for the CaM frame order test data.

This is for the recent changes to the auto-analysis with the Optimisation_settings object and for
the changes of this branch.

Speed up of the Frame_order.test_auto_analysis system test.

This involves limiting the maximum number of optimisation steps to 20 for most parts (the rigid
model excluded so the average domain position is correctly found), and using the PCS subset data for
the full data set.