relax SVN archive

Fix for the merger of the frame_order_cleanup branch.

The base CaM frame system test script, as well as th CaM frame order test data optimisation scripts
scripts, had reverted to using the old forms of the minimise.grid_search and minimise.execute user
functions.

Fix for the merger of the frame_order_cleanup branch.

The assemble_scaling_matrix() function of the specific_analyses.frame_order.parameters module was
deleted in the branch, but somehow survived the merge process.

Fix for the merger of the frame_order_cleanup branch.

Removal of an unused import, to match the branch.

Fix for the merger of the frame_order_cleanup branch.

The specific_analyses.frame_order.api module now matches that of the branch.

Fix for the merger of the frame_order_cleanup branch.

The pipe_control.pipes.check_pipe() function is being incorrectly used, but now matches that of the
frame_order_cleanup branch.

Fix for the merger of the frame_order_cleanup branch.

The data_store/__init__.py changes of r27769 were lost with the r27951 merge commit.

Merged revisions 26913-26920,26957,27240,27244,27329,27552,27609-27611,27641-27653,27663,27715,27721,27806,27878-27899,27912 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r26913 | bugman | 2014-12-03 11:09:52 +0100 (Wed, 03 Dec 2014) | 7 lines

Expanded all of the Frame_order.test_simulate_* system tests.

Two atoms have been added to the origin [0, 0, 0], one in the moving domain, the other in the
reference non-moving domain. The positions of these atoms are checked to make sure that the domain
systems are correctly handled.
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r26914 | bugman | 2014-12-03 14:38:20 +0100 (Wed, 03 Dec 2014) | 3 lines

Expanded the double rotor model description in the frame_order.select_model user function.
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r26915 | bugman | 2014-12-03 14:48:46 +0100 (Wed, 03 Dec 2014) | 5 lines

Added the pipe_name argument to the frame order check_model() function.

This is for the specific_analyses.frame_order.checks module.
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r26916 | bugman | 2014-12-03 15:08:26 +0100 (Wed, 03 Dec 2014) | 6 lines

Converted the specific_analyses.frame_order.checks module to the new Check object design.

This follows from http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions and
the changes significantly simplify the checking objects.
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r26917 | bugman | 2014-12-03 15:11:46 +0100 (Wed, 03 Dec 2014) | 6 lines

Improved checking for the frame order generate_pivot() function.

The check_model() checking object is now called to make sure the frame order model has been
specified, as this is essential for this function.
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r26918 | bugman | 2014-12-03 16:07:24 +0100 (Wed, 03 Dec 2014) | 6 lines

Created two system tests for the frame_order.simulate user function for the double rotor model.

These are Frame_order.test_simulate_double_rotor_mode1_z_axis and
Frame_order.test_simulate_double_rotor_mode2_z_axis.
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r26919 | bugman | 2014-12-03 16:21:55 +0100 (Wed, 03 Dec 2014) | 6 lines

Created two system tests for the frame_order.simulate user function for the double rotor model.

These are Frame_order.test_simulate_double_rotor_mode1_xz_plane_tilt and
Frame_order.test_simulate_double_rotor_mode2_xz_plane_tilt.
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r26920 | bugman | 2014-12-03 16:23:56 +0100 (Wed, 03 Dec 2014) | 7 lines

Added relax scripts which match the Frame_order.test_test_simulate_* system tests.

These are the tests of the frame_order.simulate user function. These were used to construct and
visually check the Brownian simulation and PDB model representation in a molecular viewer. These
could be a useful reference, so have been added to the repository.
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r26957 | bugman | 2014-12-04 13:38:43 +0100 (Thu, 04 Dec 2014) | 3 lines

Removed a debugging printout.
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r27240 | bugman | 2015-01-20 14:54:07 +0100 (Tue, 20 Jan 2015) | 7 lines

Fix for the frame order auto-analysis when only the 'rigid' model is optimised.

The final summary table printout for the number of Sobol' points used was failing as there were no
models in the table. The table is now only printed out if non rigid models are present in the model
list.
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r27244 | bugman | 2015-01-20 15:15:04 +0100 (Tue, 20 Jan 2015) | 3 lines

Copyright notice update to 2015 for the auto_analyses.frame_order module.
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r27329 | bugman | 2015-01-27 15:00:53 +0100 (Tue, 27 Jan 2015) | 7 lines

Introduced the nested_params_ave_dom_pos argument to the frame order auto-analysis.

This allows the average domain position to be set to no rotations and translations rather than
taking the average position from the rotor or free-rotor model. This can be useful when large
motions are present causing the rigid model to have unreasonable domain positions.
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r27552 | bugman | 2015-02-05 17:14:40 +0100 (Thu, 05 Feb 2015) | 6 lines

Fix for the frame_order.permute_axes user function description to allow the manual to be compiled.

The table caption containing the user function name was causing the LaTeX compilation to fail.
Therefore the captions have been rewritten to avoid the user function name.
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r27609 | bugman | 2015-02-09 13:45:17 +0100 (Mon, 09 Feb 2015) | 6 lines

Modified the frame order system test check_chi2() method to test the statistics.model user function.

This causes all of the Frame_order.test_cam_* system tests to fail, as the user function backend is
not implemented for the frame order analysis.
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r27610 | bugman | 2015-02-09 13:47:28 +0100 (Mon, 09 Feb 2015) | 6 lines

Implemented the frame order analysis backend for the statistics.model and statistics.aic user functions.

This simply required aliasing the specific analysis API common _get_model_container_cdp() method to
get_model_container().
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r27611 | bugman | 2015-02-09 15:29:08 +0100 (Mon, 09 Feb 2015) | 7 lines

Bug fix for the frame order specific analysis API base_data_loop() method.

This was looping over non-existent PCS and RDC data. Now the alignment ID is checked for in the
interatomic data container 'rdc' data structure and the spin container 'pcs' data structure, as well
as values of None, before yielding the data.
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r27641 | bugman | 2015-02-14 10:38:26 +0100 (Sat, 14 Feb 2015) | 29 lines

Created a large set of system tests for implementing the frame_order.distribute user function.

This user function will be similar to frame_order.simulate. However instead of creating a PDB file
with models from a pseudo-Brownian simulation, the frame_order.distribute user function will
generate a PDB file of models forming a uniform distribution of structures covering the full frame
order motional space.

The new system tests are:

Frame_order.test_distribute_double_rotor_mode1_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode1_z_axis
Frame_order.test_distribute_double_rotor_mode2_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode2_z_axis
Frame_order.test_distribute_free_rotor_z_axis
Frame_order.test_distribute_iso_cone_z_axis
Frame_order.test_distribute_iso_cone_xz_plane_tilt
Frame_order.test_distribute_iso_cone_torsionless_z_axis
Frame_order.test_distribute_pseudo_ellipse_xz_plane_tilt
Frame_order.test_distribute_pseudo_ellipse_z_axis
Frame_order.test_distribute_pseudo_ellipse_free_rotor_z_axis
Frame_order.test_distribute_pseudo_ellipse_torsionless_z_axis
Frame_order.test_distribute_rotor_z_axis

These are aliases for the equivalent Frame_order.test_simulate_* system tests which have had the
'type' keyword argument added, defaulting to 'sim', which allows to switch between the
frame_order.simulate and frame_order.distribute user functions. The concept behind these system
tests are the same for both user functions, so the code is shared.
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r27642 | bugman | 2015-02-14 10:54:43 +0100 (Sat, 14 Feb 2015) | 6 lines

Created the front-end of the frame_order.distribute user function.

This is a copy and modification of the frame_order.simulate user function, as the concepts are
similar.
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r27643 | bugman | 2015-02-14 10:56:30 +0100 (Sat, 14 Feb 2015) | 6 lines

Small modification of the frame_order.simulate user function.

The GUI file opening dialog wildcard selectors are now set to all PDB file types (plain text, bzip2
compressed, and gzip compressed).
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r27644 | bugman | 2015-02-14 11:22:17 +0100 (Sat, 14 Feb 2015) | 6 lines

Added the frame_order.distribute user function to the auto-analysis results output.

This will allow both the pseudo-Brownian simulation and uniform distribution PDB files to be
available to the user in all results directories (excluding the intermediate results for speed).
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r27645 | bugman | 2015-02-16 09:58:08 +0100 (Mon, 16 Feb 2015) | 9 lines

Implemented the back-end of the frame_order.distribute user function.

This follows the design of the pseudo-Brownian simulation frame_order.simulate user function. The
specific_analyses.frame_order.uf.distribute() function has been created as a modified copy of the
simulate() function of the same module. This simply performs checks and assembles the data, passing
into the new lib.frame_order.simulate.uniform_distribution() function, which itself is a modified
copy of the brownian() function in the same module.
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r27646 | bugman | 2015-02-16 10:08:49 +0100 (Mon, 16 Feb 2015) | 7 lines

Introduced the max_rotations argument into the frame_order.distribute user function.

This is used to prevent the user function from running forever. This happens whenever a cone
opening angle or torsion angle is zero, and hence the random sampling of the rotational space will
never find rotations within the motional distribution.
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r27647 | bugman | 2015-02-16 10:19:33 +0100 (Mon, 16 Feb 2015) | 6 lines

Improved control of the frame_order.distribute user function in the frame order auto-analysis.

The maximum number of rotations can now be set, and the argument for the total states for the
distribution has been shortened.
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r27648 | bugman | 2015-02-16 10:23:43 +0100 (Mon, 16 Feb 2015) | 7 lines

Speed up of the Frame_order.test_auto_analysis system test.

After the introduction of the frame_order.distribute user function into the auto-analysis, the test
was taking far too long to complete. Now the distribution arguments are set to low values to allow
the test to pass in under a minute.
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r27649 | bugman | 2015-02-16 10:25:41 +0100 (Mon, 16 Feb 2015) | 6 lines

Changed the default relax results compression type to bzip2 in the frame order auto-analysis.

This was set to no compression for speeding up some system tests, however the system tests can set
this for themselves.
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r27650 | bugman | 2015-02-16 10:26:15 +0100 (Mon, 16 Feb 2015) | 3 lines

The Frame_order.test_auto_analysis system test now sets the results file compression type to bzip2.
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r27651 | bugman | 2015-02-16 10:30:00 +0100 (Mon, 16 Feb 2015) | 5 lines

Changed the default max_rotations argument value to 100,000 in the frame_order.distribute user function.

This decrease from one million is so the user function completes in a reasonable amount of time.
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r27652 | bugman | 2015-02-16 10:35:33 +0100 (Mon, 16 Feb 2015) | 3 lines

The frame_order.distribute user function now warns when the maximum rotations are reached.
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r27653 | bugman | 2015-02-16 10:36:57 +0100 (Mon, 16 Feb 2015) | 6 lines

Deleted a number of Frame_order.test_distribute* system tests.

These are the four double rotor model tests. The frame_order.distribute user function cannot
operate on these test cases as one of the two torsion angles are set to zero in the tests.
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r27663 | bugman | 2015-02-17 17:02:40 +0100 (Tue, 17 Feb 2015) | 6 lines

Fix to allow Monte Carlo simulations to be repeated in the frame order analysis.

The code for checking for pre-existing Monte Carlo simulation data structures and raising a
RelaxError if anything is found has been deleted.
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r27715 | bugman | 2015-02-24 09:34:36 +0100 (Tue, 24 Feb 2015) | 9 lines

Fix of a fatal bug preventing the frame order analysis to be run on a multi-processor system.

The multi-processor code was calling the count_sobol_points() function of the
specific_analyses.frame_order.optimisation module to give feedback when calling the minimise.execute
or minimise.calculate user functions. However this was run in the slave command run() method, hence
would be executed on the slave. The problem is that count_sobol_points() performs a number of
checks on the current data pipe, however the slaves do not have any data pipes set up.
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r27721 | bugman | 2015-02-25 14:16:04 +0100 (Wed, 25 Feb 2015) | 7 lines

Added the new 'atom_id' argument to the frame_order.distribute user function.

This uses the new inverse selection functionality recently introduced into the trunk to delete all
structural data not matching the atom_id from the copy of the loaded structural data string prior to
generating the distribution of structures.
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r27806 | bugman | 2015-03-12 12:38:58 +0100 (Thu, 12 Mar 2015) | 12 lines

Bug fix for the frame order target function (introduced recently in r27715).

The copy.deepcopy() function is now used for all numpy input data to avoid the data from being
modified between function calls. This is important for missing RDC and PCS data which is sent in as
NaN values. In the target function __init__() method, the NaN values are replaced by 0.0 after the
self.missing_rdc and self.missing_pcs structures have been by checking for NaN values. However the
recent specific_analyses.frame_order.optimisation change in the Frame_order_minimise_command slave
command to printout the number of integration points resulted in the target function being
initialised twice, causing all NaN values to be 0.0 in the second initialisation. Hence all missing
data was being treated as real data with values of 0.0.
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r27878 | bugman | 2015-09-25 14:30:22 +0200 (Fri, 25 Sep 2015) | 3 lines

Created a new skeleton chapter in the relax manual for the frame order analysis.
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r27879 | bugman | 2015-09-25 15:10:04 +0200 (Fri, 25 Sep 2015) | 5 lines

Added a theory section to the new frame order chapter.

This is taken from an in-preparation supplement.
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r27880 | bugman | 2015-09-25 15:15:19 +0200 (Fri, 25 Sep 2015) | 6 lines

Rearrangement of the frame order chapter in the manual.

The theory section has been spun out into its own frame_order_theory.tex LaTeX file for better
organisation.
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r27881 | bugman | 2015-09-25 15:26:00 +0200 (Fri, 25 Sep 2015) | 5 lines

Fix for the previous commit (r27880).

Most chapters had been commented out and accidentally committed.
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r27882 | bugman | 2015-09-25 20:15:46 +0200 (Fri, 25 Sep 2015) | 6 lines

Added two more sections to the frame order chapter of the manual.

This includes a frame order modelling section and PCS numerical integration section. Both are from
a supplement from an in-preparation manuscript.
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r27883 | bugman | 2015-09-25 20:26:01 +0200 (Fri, 25 Sep 2015) | 3 lines

Added a DOI and ISBN number to the bibliography.
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r27884 | bugman | 2015-09-28 18:13:54 +0200 (Mon, 28 Sep 2015) | 3 lines

Moved the frame_order_theory.tex LaTeX file into the frame_order directory.
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r27885 | bugman | 2015-09-28 18:37:31 +0200 (Mon, 28 Sep 2015) | 3 lines

Shifted the frame order model derivations into their own 'Advanced topics' chapter.
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r27886 | bugman | 2015-09-28 19:05:02 +0200 (Mon, 28 Sep 2015) | 3 lines

Cross-referencing fix.
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r27887 | bugman | 2015-09-29 13:51:04 +0200 (Tue, 29 Sep 2015) | 3 lines

Added the frame order sample scripts used in the CaM-IQ analysis.
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r27888 | bugman | 2015-09-29 16:02:20 +0200 (Tue, 29 Sep 2015) | 3 lines

Added an introduction for the frame order chapter of the manual.
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r27889 | bugman | 2015-09-29 16:15:49 +0200 (Tue, 29 Sep 2015) | 5 lines

Added a 'Data analysis' section to the frame order chapter of the manual.

This includes the N-state and frame order analysis scripts required to perform a full analysis.
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r27890 | bugman | 2015-09-29 17:43:04 +0200 (Tue, 29 Sep 2015) | 6 lines

Editing of the data analysis section of the frame order chapter of the manual.

A PCS structural error figure has been added, all the text improved, and the scripts made to match
those in sample_scripts/frame_order/.
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r27891 | bugman | 2015-09-29 18:09:20 +0200 (Tue, 29 Sep 2015) | 3 lines

Added a section to the end of the frame order chapter about the long computation times.
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r27892 | bugman | 2015-09-29 18:17:13 +0200 (Tue, 29 Sep 2015) | 5 lines

The 'scons clean' target now removes all LaTeX *.aux files.

The docs/latex/frame_order/ directory is now also being checked for *.aux files.
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r27893 | bugman | 2015-09-29 18:17:47 +0200 (Tue, 29 Sep 2015) | 3 lines

Trailing whitespace removal in the full_analysis.py frame order sample script.
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r27894 | bugman | 2015-09-29 18:23:52 +0200 (Tue, 29 Sep 2015) | 3 lines

Removed many unnecessary references to relax.
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r27895 | bugman | 2015-09-29 18:26:10 +0200 (Tue, 29 Sep 2015) | 3 lines

Removed lots of useless comments about book references.
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r27896 | bugman | 2015-09-29 18:43:07 +0200 (Tue, 29 Sep 2015) | 3 lines

Reference fix in the frame order chapter of the manual.
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r27897 | bugman | 2015-09-29 19:00:06 +0200 (Tue, 29 Sep 2015) | 3 lines

Added some images missing from the frame order chapter of the manual.
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r27898 | bugman | 2015-09-29 19:02:32 +0200 (Tue, 29 Sep 2015) | 3 lines

Avoided a doubly defined label in the manual.
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r27899 | bugman | 2015-09-29 19:06:50 +0200 (Tue, 29 Sep 2015) | 5 lines

Removed some duplicated text in the frame order models chapter of the manual.

This is duplicated from the frame order analysis chapter.
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r27912 | bugman | 2015-10-01 14:59:38 +0200 (Thu, 01 Oct 2015) | 3 lines

Indentation fix for allowing the API documentation to be properly compiled.
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Merged revisions 26896-26900,26908-26911 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r26896 | bugman | 2014-12-02 16:02:05 +0100 (Tue, 02 Dec 2014) | 6 lines

Created the Frame_order.test_simulate_iso_cone_xz_plane_tilt system test.

This is to check the frame_order.simulate user function for the torsionless isotropic cone model
with a xz-plane tilt.
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r26897 | bugman | 2014-12-02 16:12:07 +0100 (Tue, 02 Dec 2014) | 6 lines

Created the Frame_order.test_simulate_pseudo_ellipse_free_rotor_z_axis system test.

This is to check the frame_order.simulate user function for the free rotor pseudo-ellipse model
along the z-axis.
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r26898 | bugman | 2014-12-02 16:16:33 +0100 (Tue, 02 Dec 2014) | 6 lines

Created the Frame_order.test_simulate_pseudo_ellipse_xy_plane_tilt system test.

This is to check the frame_order.simulate user function for the pseudo-ellipse model with a xz-plane
tilt.
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r26899 | bugman | 2014-12-02 16:29:04 +0100 (Tue, 02 Dec 2014) | 6 lines

Created the Frame_order.test_simulate_pseudo_ellipse_torsionless_z_axis system test.

This is to check the frame_order.simulate user function for the torsionless pseudo-ellipse model
along the z-axis.
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r26900 | bugman | 2014-12-02 16:29:57 +0100 (Tue, 02 Dec 2014) | 5 lines

Fix for the Frame_order.test_simulate_pseudo_ellipse_xz_plane_tilt system test name.

This was mislabelled as Frame_order.test_simulate_pseudo_ellipse_xy_plane_tilt.
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r26908 | bugman | 2014-12-03 09:34:46 +0100 (Wed, 03 Dec 2014) | 8 lines

Redesign of the pymol.frame_order user function.

This user function was still fitting to the old design in the relax trunk. It has been updated for
the frame_order_cleanup branch whereby the frame_order.pdb_model user function has been split up and
the positional distribution has been replaced by the Brownian simulation user function
frame_order.simulate.
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r26909 | bugman | 2014-12-03 10:03:50 +0100 (Wed, 03 Dec 2014) | 6 lines

Better checking for the non-moving domain setup.

The frame_order.pdb_model user function will now raise a RelaxError if the frame_order.ref_domain
user function has not been called to set up the non-moving domain.
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r26910 | bugman | 2014-12-03 10:13:17 +0100 (Wed, 03 Dec 2014) | 6 lines

Updated the frame_order.ref_domain user function for the current branch design.

This user function was quite out of date. The alignment tensor checks have been removed, to allow
this to be used in the absence of base data. And the user function description has been updated.
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r26911 | bugman | 2014-12-03 10:25:58 +0100 (Wed, 03 Dec 2014) | 3 lines

Updated all frame order system tests for the frame_order.ref_domain user function requirement.
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Merged revisions 26671,26673,26675-26678,26680,26683-26698,26717-26722,26764,26767,26773,26784,26789,26796-26797,26800-26802,26809 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r26671 | bugman | 2014-11-20 18:41:46 +0100 (Thu, 20 Nov 2014) | 7 lines

Completed the Frame_order.test_pdb_model_rotor system test.

This now sets the rotor axis to the z-axis (with a printout to be sure), sets the torsion angle to
zero for simplicity, creates a new data pipe and loads the PDB representation file, then checks all
of the key atom coordinates.
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r26673 | bugman | 2014-11-20 19:25:40 +0100 (Thu, 20 Nov 2014) | 9 lines

Fixes for the unit tests of the lib.frame_order_matrix_ops module for the free rotor isotropic cone.

The S1 order parameter has been eliminated due to angles > pi/2.0 causing the frame order matrix to
be incorrectly predicted. Therefore all unit tests have been converted to use the cone opening
angle theta instead. In addition, the test_compile_2nd_matrix_iso_cone_free_rotor_disorder had been
modified to pass with the incorrect frame order matrix by comparing to the half cone frame order
matrix rather than the identity frame order matrix.
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r26675 | bugman | 2014-11-21 08:44:35 +0100 (Fri, 21 Nov 2014) | 3 lines

Fix for inverted axes in the new Frame_order.test_pdb_model_rotor system test.
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r26676 | bugman | 2014-11-21 08:58:39 +0100 (Fri, 21 Nov 2014) | 12 lines

Huge bug fix for the frame_order.pdb_model user function - the single axis direction was incorrect.

In the PDB representation of the frame order motion for the rotor and isotropic cone models (rotor,
free rotor, isotropic cone, free rotor isotropic cone, and torsionless isotropic cone), the X and Z
axes were swapped. This is because the eigenframe of the motion was being incorrectly constructed
via the lib.geometry.rotations.two_vect_to_R() function.

For better control, the specific_analyses.frame_order.geometric.frame_from_axis() function has been
created. This constructs a full motional eigenframe from the Z-axis. The problem was detected via
the new Frame_order.test_pdb_model_rotor system test.
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r26677 | bugman | 2014-11-21 09:08:44 +0100 (Fri, 21 Nov 2014) | 9 lines

Size fix for the rotor representation from the frame_order.pdb_model user function.

The size problem was detected via the Frame_order.test_pdb_model_rotor system test. The rotors in
the PDB representation were all fixed in size, and ignored the 'size' argument of the
frame_order.pdb_model user function. The size argument is now passed into the add_rotors() function
of the specific_analyses.frame_order.geometric and passed on to the rotor() function of the
lib.structure.represent.rotor module.
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r26678 | bugman | 2014-11-21 09:41:51 +0100 (Fri, 21 Nov 2014) | 6 lines

Created the Frame_order.test_pdb_model_rotor2 system test to check for an offset pivot.

The pivot is set to [1, 0, 1] so that the rotor axis is tilted -45 degrees in the xz-plane. And the
size of the geometric object is set to 100 Angstrom for better testing of the sizes of the elements.
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r26680 | bugman | 2014-11-21 10:23:38 +0100 (Fri, 21 Nov 2014) | 5 lines

Simplification of the Frame_order.test_pdb_model_rotor system test.

The size is now programatically handled.
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r26683 | bugman | 2014-11-21 10:51:43 +0100 (Fri, 21 Nov 2014) | 6 lines

Created the Frame_order.test_pdb_model_iso_cone system test.

This is for checking the PDB representation of the isotropic cone frame order model created by the
frame_order.pdb_model user function. It checks both A and B representations.
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r26684 | bugman | 2014-11-21 10:55:28 +0100 (Fri, 21 Nov 2014) | 6 lines

Fix for the cone sized created by the frame_order.pdb_model user function.

The 'size' argument was not being used at all for the cone size. It is now passed into the
lib.structure.represent.cone.cone() function as the 'scale' argument.
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r26685 | bugman | 2014-11-21 10:59:22 +0100 (Fri, 21 Nov 2014) | 3 lines

Small fix for the Frame_order.test_pdb_model_iso_cone system test for the 'B' representation.
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r26686 | bugman | 2014-11-21 11:01:09 +0100 (Fri, 21 Nov 2014) | 6 lines

Fix for the representation label positions created by the frame_order.pdb_model user function.

The 'size' argument was not being used at all for the representation title
atoms. It is now passed into the add_titles() function as the displacement argument + 10 Angstrom.
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r26687 | bugman | 2014-11-21 11:04:19 +0100 (Fri, 21 Nov 2014) | 3 lines

Printout fix for the axis in the Frame_order.test_pdb_model_iso_cone system test.
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r26688 | bugman | 2014-11-21 13:46:14 +0100 (Fri, 21 Nov 2014) | 6 lines

Created the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test.

This checks the PDB file from the frame_order.pdb_model user function for the isotropic cone model
with a xz-plane tilt.
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r26689 | bugman | 2014-11-21 13:49:58 +0100 (Fri, 21 Nov 2014) | 3 lines

Renamed all of the Frame_order.test_pdb_model_* system tests to be more descriptive.
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r26690 | bugman | 2014-11-21 15:00:10 +0100 (Fri, 21 Nov 2014) | 7 lines

Improvements for all of the Frame_order.test_pdb_model_* system tests.

The rotate_from_Z() method has been introduced to simplify the determination of the 3D coordinates
expected for the PDB file. This will allow for more advanced testing of the PDB for the cone
models.
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r26691 | bugman | 2014-11-21 15:32:08 +0100 (Fri, 21 Nov 2014) | 3 lines

Fixes for the printouts from the Frame_order.test_pdb_model_rotor_* system tests.
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r26692 | bugman | 2014-11-21 16:37:00 +0100 (Fri, 21 Nov 2014) | 3 lines

Alphabetical ordering of the Frame_order system test methods.
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r26693 | bugman | 2014-11-21 17:45:39 +0100 (Fri, 21 Nov 2014) | 6 lines

Fixes for all of the Frame_order system tests - the temporary directories are now being deleted.

The system test base class tearDown() method is now being called to properly clean up after the
tests.
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r26694 | bugman | 2014-11-21 18:07:06 +0100 (Fri, 21 Nov 2014) | 6 lines

Created the Frame_order.test_pdb_model_pseudo_ellipse_z_axis system test.

This demonstrates the correct atom coordinates in the PDB file created by the frame_order.pdb_model
user function for the pseudo-ellipse model along the z-axis.
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r26695 | bugman | 2014-11-21 18:09:17 +0100 (Fri, 21 Nov 2014) | 6 lines

Fixes for the checks in the Frame_order.test_pdb_model_* system tests.

Atomic positions are now checked with self.assertAlmostEqual() to 3 places, and the residue and atom
names and numbers are checked with self.assertEqual().
........
r26696 | bugman | 2014-11-21 19:19:53 +0100 (Fri, 21 Nov 2014) | 7 lines

Created the Frame_order.test_pdb_model_pseudo_ellipse_xz_plane_tilt system test.

This checks the PDB file created by the frame_order.pdb_model user function for the pseudo-ellipse
model with a xz-plane tilt. To properly construct the coordinates, the rotate_from_Z() method was
modified to accept a rotation matrix argument to allow the geometric shape to be rotated.
........
r26697 | bugman | 2014-11-21 19:32:37 +0100 (Fri, 21 Nov 2014) | 6 lines

Modified the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test to have a cone angle.

The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB
file for a cone opening half-angle of 2.0.
........
r26698 | bugman | 2014-11-21 19:51:14 +0100 (Fri, 21 Nov 2014) | 6 lines

Modified the Frame_order.test_pdb_model_iso_cone_z_axis system test to have a cone angle.

The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB
file for a cone opening half-angle of 2.0.
........
r26717 | bugman | 2014-11-25 15:32:07 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new system tests for the free rotor PDB representation file.

This is the file from the frame_order.pdb_model user function. The two new unit tests are
Frame_order.test_pdb_model_free_rotor_z_axis and
Frame_order.test_pdb_model_free_rotor_xz_plane_tilt.
........
r26718 | bugman | 2014-11-25 16:14:06 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new frame order system tests for the free rotor isotropic cone PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_iso_cone_free_rotor_z_axis and
Frame_order.test_pdb_model_iso_cone_free_rotor_xz_plane_tilt.
........
r26719 | bugman | 2014-11-25 16:29:52 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new frame order system tests for the torsionless isotropic cone PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_iso_cone_torsionless_z_axis and
Frame_order.test_pdb_model_iso_cone_torsionless_xz_plane_tilt.
........
r26720 | bugman | 2014-11-25 16:39:03 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new frame order system tests for the free rotor pseudo-ellipse PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_xz_plane_tilt.
........
r26721 | bugman | 2014-11-25 16:56:10 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new frame order system tests for the torsionless pseudo-ellipse PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_torsionless_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_torsionless_xz_plane_tilt.
........
r26722 | bugman | 2014-11-25 19:39:46 +0100 (Tue, 25 Nov 2014) | 7 lines

Created two new frame order system tests for the double rotor PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_double_rotor_z_axis and
Frame_order.test_pdb_model_double_rotor_xz_plane_tilt.
........
r26764 | bugman | 2014-11-26 14:35:38 +0100 (Wed, 26 Nov 2014) | 6 lines

Added relax scripts and PDB files which match the Frame_order.test_test_pdb_model_* system tests.

These were used to construct and visually check the tests in a molecular viewer. These could be a
useful reference, so have been added to the repository.
........
r26767 | bugman | 2014-11-26 15:55:07 +0100 (Wed, 26 Nov 2014) | 7 lines

Simplified all of the Frame_order.test_pdb_model_* system tests.

The atom, residue and 3D coordinate checking in all these methods has been shifted into the common
check_pdb_model_representation() method. This dramatically decreases the amount of code in the
system test file.
........
r26773 | bugman | 2014-11-27 10:54:56 +0100 (Thu, 27 Nov 2014) | 7 lines

Simplification for all of the Frame_order.test_pdb_model_* system tests.

The model setup in all of these tests has been merged into the common setup_model() method. This
not only removes a large quantity of repetitive code, but the new method can also be used for
constructing future tests, for example for checking the frame_order.simulate user function.
........
r26784 | bugman | 2014-11-27 16:27:21 +0100 (Thu, 27 Nov 2014) | 6 lines

Created an initial version of the Frame_order.test_simulate_rotor_z_axis system test.

This is to check the frame_order.simulate user function rotor model along the z-axis. It currently
fails due to a bug in the user function.
........
r26789 | bugman | 2014-11-27 17:56:25 +0100 (Thu, 27 Nov 2014) | 8 lines

Fixes for the Frame_order.test_simulate_rotor_z_axis system test.

Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is
required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at
[1, 0, 0] so that the axis alpha angle of pi/2 creates an axis parallel to Z. The origin to atom
distance check has also been loosened due to the PDB truncation artifact.
........
r26796 | bugman | 2014-11-28 08:50:00 +0100 (Fri, 28 Nov 2014) | 8 lines

Fix for the Frame_order.test_pdb_model_free_rotor_xz_plane_tilt system test.

This was broken while implementing the Frame_order.test_simulate_rotor_z_axis system test. Instead
of shifting the 6 atom structure so its CoM is the pivot of the motion when creating the atoms, now
the Frame_order.test_simulate_rotor_z_axis system test sets the average domain translation vector to
the pivot to achieve the same result. This preserves the z-axis orientation of the rotor models.
........
r26797 | bugman | 2014-11-28 08:55:30 +0100 (Fri, 28 Nov 2014) | 5 lines

Created the Frame_order.test_simulate_free_rotor_z_axis system test.

This is to check the frame_order.simulate user function for the free rotor model along the z-axis.
........
r26800 | bugman | 2014-11-28 12:15:34 +0100 (Fri, 28 Nov 2014) | 6 lines

Created the Frame_order.test_simulate_iso_cone_z_axis system test.

This is to check the frame_order.simulate user function for the isotropic cone model along the
z-axis.
........
r26801 | bugman | 2014-11-28 12:17:42 +0100 (Fri, 28 Nov 2014) | 6 lines

Created the Frame_order.test_simulate_iso_cone_free_rotor_z_axis system test.

This is to check the frame_order.simulate user function for the free rotor isotropic cone model
along the z-axis.
........
r26802 | bugman | 2014-11-28 12:20:00 +0100 (Fri, 28 Nov 2014) | 6 lines

Created the Frame_order.test_simulate_iso_cone_torsionless_z_axis system test.

This is to check the frame_order.simulate user function for the torsionless isotropic cone model
along the z-axis.
........
r26809 | bugman | 2014-11-28 15:36:21 +0100 (Fri, 28 Nov 2014) | 6 lines

Created the Frame_order.test_simulate_pseudo_ellipse_z_axis system test.

This is to check the frame_order.simulate user function for the pseudo-ellipse model along the
z-axis.
........

Merged revisions 26141,26207,26313-26320,26349,26365,26388-26394,26396-26477,26479-26481,26484,26534-26537,26657-26658,26668-26669 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r26141 | bugman | 2014-10-02 15:53:19 +0200 (Thu, 02 Oct 2014) | 5 lines

Modified the PCS content testing base system.

The paramagnetic centre is now shifted to the origin, as this is the real centre of the PCS physics.
........
r26207 | bugman | 2014-10-08 12:10:04 +0200 (Wed, 08 Oct 2014) | 17 lines

Intermediate optimisation results are now stored by the frame order auto-analysis.

The results from each minimise.grid_search and minimise.execute user function call are now stored in
specially named directories located in the 'intermediate_results' directory, which itself is located
in the auto-analysis results_dir directory. This allows intermediate results to be more easily
analysed later on, which can be useful for optimising the optimisation steps. These directories can
also be used for the pre_run_dir auto-analysis argument for subsequent refinements from earlier
steps in the optimisation. The results stored include everything from the results_output() method
and the count_sobol_points() and summarise() functions.

To allow this to work, the auto-analysis functions count_sobol_points() and summarise() required
modification. Results files are now always loaded into a temporary data pipe, rather switching to
the corresponding pipe, and the temporary data pipe is deleted after the data has been extracted.
The original data pipe name is also stored and a switch back to that pipe occurs at the end of each
function.
........
r26313 | bugman | 2014-10-20 09:54:11 +0200 (Mon, 20 Oct 2014) | 7 lines

The simulation is now turned of for intermediate results in the frame order auto-analysis.

The intermediate results are only for checking, so for these the full pseudo-Brownian dynamics
simulations are not required. The simulation flag has been introduced into the results_output()
method of the auto-analysis to control this.
........
r26314 | bugman | 2014-10-20 11:52:52 +0200 (Mon, 20 Oct 2014) | 8 lines

The splitting of the rigid model grid search into rotation and translation parts is now optional.

In the frame order auto-analysis, the rigid_grid_split argument has been introduced. The
alternating algorithm of performing a grid search over the rotational space followed by translation
is now optional and turned off by default. The reason is because the global minimum is sometimes
missed with this shortcut algorithm.
........
r26315 | bugman | 2014-10-20 14:45:24 +0200 (Mon, 20 Oct 2014) | 6 lines

Speed up of the Frame_order.test_auto_analysis system test.

The splitting of the rigid model grid search into rotation and translation parts has been
reactivated.
........
r26316 | bugman | 2014-10-20 15:11:58 +0200 (Mon, 20 Oct 2014) | 5 lines

Created the Optimisation.has_grid() method for the frame order auto-analysis.

This is used to test if the optimisation settings object has a grid search defined.
........
r26317 | bugman | 2014-10-20 15:15:21 +0200 (Mon, 20 Oct 2014) | 7 lines

The grid search can now be skipped for the rigid model in the frame order auto-analysis.

If the input 3D structures are close to the real solution, the grid search over the translational
and rotation parameters of the rigid model could be skipped. This speeds up the analysis and can
help find the real solution in problematic cases.
........
r26318 | bugman | 2014-10-20 16:23:08 +0200 (Mon, 20 Oct 2014) | 6 lines

The intermediate results storing can now be turned off in the frame order auto-analysis.

The new store_intermediate Boolean argument has been added to the analysis to allow the storage of
these results to be turned on or off.
........
r26319 | bugman | 2014-10-20 16:24:11 +0200 (Mon, 20 Oct 2014) | 5 lines

The intermediate results are no longer stored in the Frame_order.test_auto_analysis system test.

This drops the test timing on one system from ~190 seconds to ~50 seconds.
........
r26320 | bugman | 2014-10-20 16:45:49 +0200 (Mon, 20 Oct 2014) | 7 lines

The compression level for results files can now be set in the frame order auto-analysis.

This is via the new argument results_compress_type, which is used to set the compress_type argument
of the results.write user function. The results reading parts of the auto-analysis have been
updated to allow uncompressed, bzip2 compressed, and gzip compressed files to be handled.
........
r26349 | bugman | 2014-10-22 15:22:03 +0200 (Wed, 22 Oct 2014) | 7 lines

Added a printout of the frame order model in the target function setup function.

This is printed out when the minimise.calculate, minimise.grid_search, or minimise.execute user
function are called, and is for better feedback, especially in the auto-analysis where the
repetitive optimisations can be confusing.
........
r26365 | bugman | 2014-10-23 11:34:29 +0200 (Thu, 23 Oct 2014) | 6 lines

Updated the frame order analysis for the structure.load_spins user function changes.

The minimise_setup_atomic_pos() function of the specific_analyses.frame_order.optimisation module
now handles the mixed type spin.pos variable correctly.
........
r26388 | bugman | 2014-10-23 15:32:59 +0200 (Thu, 23 Oct 2014) | 5 lines

The data pipe containing a PCS subset is now optional in the frame order auto-analysis.

This is for systems which have so little data that a subset makes no sense.
........
r26389 | bugman | 2014-10-23 15:47:26 +0200 (Thu, 23 Oct 2014) | 3 lines

Missing import.
........
r26390 | bugman | 2014-10-23 15:57:02 +0200 (Thu, 23 Oct 2014) | 12 lines

Redesigned the optimisation steps for the frame order auto-analysis.

The code has been significantly simplified as the optimisation for the PCS subset and full data set
was the same. The code duplication has been eliminated by combining it into the new optimisation()
method. The check for the PCS subset has also been expanded so that it is skipped if the subset
data pipe is not supplied, even if an optimisation object for the subset has been (this should
prevent strange errors when the auto-analysis is incorrectly used).

A side effect of this code merger is that the zooming grid search has now been activated for the
full PCS data set. This is of great benefit when a PCS subset is not being used.
........
r26391 | bugman | 2014-10-23 16:19:39 +0200 (Thu, 23 Oct 2014) | 6 lines

The minimise.execute user function skip_preset flag is now False in the frame order auto-analysis.

This is for the main model optimisation. Without this flag set, the grid search for the pivot point
position for the rotor model was being skipped at the first zoom level.
........
r26392 | bugman | 2014-10-23 16:32:15 +0200 (Thu, 23 Oct 2014) | 9 lines

The pivot point can now be excluded from the grid search in the frame order auto-analysis.

If the initial pivot point is known to be reasonable, then it may be possible to skip it in the grid
search for the rotor frame order model. This can lead to a speed up of the analysis and can help
with stability. The pivot_search argument has been added to the auto-analysis
Optimisation.add_grid() method to enable this. The get_grid_pivot_search() method has also been
added to allow the auto-analysis to query this and turn it off if desired.
........
r26393 | bugman | 2014-10-28 11:24:45 +0100 (Tue, 28 Oct 2014) | 5 lines

Updated the description of the frame_order.permute_axes user function.

This now includes the isotopic cone.
........
r26394 | bugman | 2014-10-28 14:23:43 +0100 (Tue, 28 Oct 2014) | 6 lines

Replaced the table in the frame_order.permute_axes user function.

The original table was an old and incorrect version. This has been replaced by the correct
permutation table.
........
r26396 | bugman | 2014-11-01 12:36:07 +0100 (Sat, 01 Nov 2014) | 7 lines

Added some old relax scripts for both simulating and predicting the frame order matrix elements.

These were used for the initial implementation of the pseudo-ellipse frame order model back in July
2010. The scripts will be extended for all frame order models. The simulated values could then be
used in unit tests of the frame order matrix code in lib.frame_order.
........
r26397 | bugman | 2014-11-01 14:09:17 +0100 (Sat, 01 Nov 2014) | 6 lines

Updated the frame_order_simulate.py script for simulating frame order matrix elements.

The MODEL variable has been added in preparation for supporting all model types, and this is now
added to the file name. The Grace header is now also being automatically generated.
........
r26398 | bugman | 2014-11-01 14:42:40 +0100 (Sat, 01 Nov 2014) | 5 lines

Improvements for the Grace files produced by the frame_order_simulate.py script.

The model name is now set as a variable and is used for the subheading.
........
r26399 | bugman | 2014-11-01 14:44:03 +0100 (Sat, 01 Nov 2014) | 7 lines

Updated the frame_order_solution.py script for directly calculating the frame order matrix elements.

The MODEL variable has been added in preparation for supporting all model types, and this is now
added to the file name. The Grace header is now also being automatically generated and this matches
that for the frame_order_simulation.py script.
........
r26400 | bugman | 2014-11-01 17:00:00 +0100 (Sat, 01 Nov 2014) | 5 lines

Zero values can now be handled in the pseudo-ellipse 1st degree frame order matrix function.

This is in lib.frame_order.pseudo_ellipse.compile_1st_matrix_pseudo_ellipse().
........
r26401 | bugman | 2014-11-01 17:01:58 +0100 (Sat, 01 Nov 2014) | 7 lines

Removed some unused code in the pseudo-ellipse 2nd degree frame order matrix function.

This is the compile_2nd_matrix_pseudo_ellipse() function in the lib.frame_order.pseudo_ellipse
module. The change should make the RDC part of the frame order analysis for the pseudo-ellipse
model slightly faster.
........
r26402 | bugman | 2014-11-01 17:57:15 +0100 (Sat, 01 Nov 2014) | 5 lines

Modified the rotate_daeg() function as this is independent of the degree of the frame order matrix.

This is the lib.frame_order.matrix_ops.rotate_daeg() function.
........
r26403 | bugman | 2014-11-01 18:00:21 +0100 (Sat, 01 Nov 2014) | 6 lines

Fix for the compile_1st_matrix_pseudo_ellipse() function.

This function of the lib.frame_order.pseudo_ellipse module now can rotate the 1st degree frame order
matrix out of its eigenframe and into the PDB frame.
........
r26404 | bugman | 2014-11-01 18:02:31 +0100 (Sat, 01 Nov 2014) | 5 lines

Created an executable Python script for mass converting the frame order matrix Grace graphs.

The script converts the *.agr files to EPS and PNG files.
........
r26405 | bugman | 2014-11-01 18:04:10 +0100 (Sat, 01 Nov 2014) | 6 lines

Modified the frame order matrix Grace graph to EPS/PNG format conversion script.

The binary being called is now 'grace' rather than 'xmgrace'. This allows different Grace versions
to be used.
........
r26406 | bugman | 2014-11-01 20:13:38 +0100 (Sat, 01 Nov 2014) | 6 lines

Modified the frame order matrix Grace graph to EPS/PNG format conversion script.

Grace is now used to create a PostScript file and then the ps2eps program is called to convert to
EPS. This produces much better EPS files for inclusion into LaTeX documents.
........
r26407 | bugman | 2014-11-01 20:22:26 +0100 (Sat, 01 Nov 2014) | 8 lines

Redesign of the frame_order_solution.py script for calculating the frame order matrix elements.

This script now loops over all models, all motional frame orientations, and all order parameters to
generate the Grace graphs of all 1st and 2nd degree frame order matrix elements. Therefore the
script only needs to be executed once. The script also now calculates a point at zero (slightly
shifted to 0.01 to avoid artifacts).
........
r26408 | bugman | 2014-11-01 20:24:24 +0100 (Sat, 01 Nov 2014) | 6 lines

Added all of the Grace graphs produced by the frame_order_solution.py script.

These are the graphs of the 1st and 2nd degree frame order matrix elements, calculated using the
functions in lib.frame_order.
........
r26409 | bugman | 2014-11-02 15:39:25 +0100 (Sun, 02 Nov 2014) | 8 lines

Updated frame_order_simulate.py to be much faster in simulating the frame order matrix elements.

The script also matches the Grace file output of the frame_order_solution.py script. The inside()
method has been renamed for the pseudo-ellipse and the infrastructure for adding support for the
other frame order models has been added. By shifting calculations outside of the loops, the script
is now many orders of magnitude faster.
........
r26410 | bugman | 2014-11-02 22:14:36 +0100 (Sun, 02 Nov 2014) | 4 lines

Implemented the compile_1st_matrix_rotor() function.

This is for the lib.frame_order.rotor module. The function will calculate the 1st degree in-frame
frame order matrix for the rotor model.
........
r26411 | bugman | 2014-11-02 22:14:38 +0100 (Sun, 02 Nov 2014) | 4 lines

Created the Grace graphs for the rotor model 1st degree frame order matrix elements.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26412 | bugman | 2014-11-02 22:14:41 +0100 (Sun, 02 Nov 2014) | 4 lines

Implemented the compile_1st_matrix_free_rotor() function.

This is for the lib.frame_order.free_rotor module. The function will calculate the 1st degree
in-frame frame order matrix for the free rotor model.
........
r26413 | bugman | 2014-11-02 22:14:43 +0100 (Sun, 02 Nov 2014) | 4 lines

Created the Grace graphs for the free rotor model 1st degree frame order matrix elements.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26414 | bugman | 2014-11-02 22:14:45 +0100 (Sun, 02 Nov 2014) | 4 lines

Implemented the compile_1st_matrix_iso_cone() function.

This is for the lib.frame_order.iso_cone module. The function will calculate the 1st degree
in-frame frame order matrix for the isotropic cone model.
........
r26415 | bugman | 2014-11-02 22:14:48 +0100 (Sun, 02 Nov 2014) | 4 lines

Created the Grace graphs for the isotropic cone model 1st degree frame order matrix elements.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26416 | bugman | 2014-11-02 22:14:50 +0100 (Sun, 02 Nov 2014) | 4 lines

Implemented the compile_1st_matrix_iso_cone_torsionless() function.

This is for the lib.frame_order.iso_cone_torsionless module. The function will calculate the 1st
degree in-frame frame order matrix for the torsionless isotropic cone model.
........
r26417 | bugman | 2014-11-02 22:14:52 +0100 (Sun, 02 Nov 2014) | 4 lines

Created the Grace graphs for the torsionless isotropic cone 1st degree frame order matrix elements.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26418 | bugman | 2014-11-02 22:14:55 +0100 (Sun, 02 Nov 2014) | 4 lines

Implemented the compile_1st_matrix_iso_cone_free_rotor() function.

This is for the lib.frame_order.iso_cone_free_rotor module. The function will calculate the 1st
degree in-frame frame order matrix for the free rotor isotropic cone model.
........
r26419 | bugman | 2014-11-02 22:14:57 +0100 (Sun, 02 Nov 2014) | 4 lines

Created the Grace graphs for the free rotor isotropic cone 1st degree frame order matrix elements.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26420 | bugman | 2014-11-02 22:14:59 +0100 (Sun, 02 Nov 2014) | 1 line

Docstring fixes for the new compile_1st_matrix_iso_cone() function.
........
r26421 | bugman | 2014-11-02 22:45:54 +0100 (Sun, 02 Nov 2014) | 4 lines

A minor speed up for the frame_order_simulate.py script.

The angles are now being calculated at the very start prior to the main loop, removing repetitive
calculations.
........
r26422 | bugman | 2014-11-02 22:45:56 +0100 (Sun, 02 Nov 2014) | 5 lines

The frame_order_simulate.py script now uses lib.text.progress.progress_meter().

This script for simulating the frame order matrix elements now uses the standard progress meter in
relax to simplify the script. This should also speed up the calculations as the progress printouts
were slowing down the calculations.
........
r26423 | bugman | 2014-11-03 08:18:07 +0100 (Mon, 03 Nov 2014) | 7 lines

Simulation of the pseudo-ellipse frame order matrix elements.

This is for a simulation of 1,000,000 states for each angle increment, and includes in-frame and
out-of-frame and varying of theta X, Y, and Z. The resultant Grace graphs have been added to the
repository.
........
r26424 | bugman | 2014-11-03 08:31:48 +0100 (Mon, 03 Nov 2014) | 4 lines

The frame order matrix element simulation script now uses the Kronecker outer product.

This allows the frame order matrix to be in the same notation as that used internally in relax. It
will cause the colours of the Sijkl_* curves to match between the simulation and solution scripts.
........
r26425 | bugman | 2014-11-06 13:47:49 +0100 (Thu, 06 Nov 2014) | 7 lines

Added the rotor model to the frame order matrix element simulation script.

The generated in-frame and out-of-frame Grace graphs containing the matrix values for 1,000,000
simulation values have been added to the repository. The script was modified so that the rotation
is generated by special rotation_*() methods which are aliased depending on the model.
........
r26426 | bugman | 2014-11-06 14:07:28 +0100 (Thu, 06 Nov 2014) | 7 lines

Added the free rotor model to the frame order matrix element simulation script.

The generated in-frame and out-of-frame Grace graphs containing the matrix values for 1,000,000
simulation values have been added to the repository. The inside_free_rotor() method has been added
to always return True for the rotation generated by rotation_z_axis().
........
r26427 | bugman | 2014-11-06 15:48:03 +0100 (Thu, 06 Nov 2014) | 6 lines

Simplifications and fixes for the 1st degree frame order matrix calculation for the pseudo-ellipse.

The compile_1st_matrix_pseudo_ellipse() function of the lib.frame_order.pseudo_ellipse module has
been significantly simplified by shifting a lot of maths outside of the quadratic integration.
........
r26428 | bugman | 2014-11-06 15:49:09 +0100 (Thu, 06 Nov 2014) | 5 lines

Updated all the calculated 1st degree frame order matrix graphs for the pseudo-ellipse.

The changes are due to the fixes in the lib.frame_order.pseudo_ellipse module.
........
r26429 | bugman | 2014-11-06 19:49:04 +0100 (Thu, 06 Nov 2014) | 3 lines

Simplifications for all of the torsionless pseudo-ellipse frame order matrix equations.
........
r26430 | bugman | 2014-11-06 20:00:00 +0100 (Thu, 06 Nov 2014) | 6 lines

Implemented the compile_1st_matrix_pseudo_ellipse_torsionless() function.

This is for the lib.frame_order.pseudo_ellipse_torsionless module. The function will calculate the
1st degree in-frame frame order matrix for the torsionless pseudo-ellipse model.
........
r26431 | bugman | 2014-11-06 20:01:37 +0100 (Thu, 06 Nov 2014) | 6 lines

Created the Grace graphs for the torsionless pseudo-ellipse model 1st degree frame order matrix.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
........
r26432 | bugman | 2014-11-07 09:00:59 +0100 (Fri, 07 Nov 2014) | 8 lines

Added the isotropic cone model to the frame order matrix element simulation script.

The generated in-frame and out-of-frame Grace graphs for the torsion angle cone_sigma_max,
containing the matrix values for 1,000,000 simulation values have been added to the repository. The
inside_iso_cone() method has been created to check for the theta_x and theta_z angle violations from
the rotation_hypersphere() method.
........
r26433 | bugman | 2014-11-07 09:08:23 +0100 (Fri, 07 Nov 2014) | 7 lines

Simplifications for the inside_*() methods of the frame order matrix element simulation script.

The limit() method is now called only once outside of these methods and the maximum cone half-angles
passed into the inside_*() methods. Although only slightly faster, this is mainly to simplify the
code.
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r26434 | bugman | 2014-11-07 09:09:39 +0100 (Fri, 07 Nov 2014) | 3 lines

Alphabetical ordering of methods in the frame order matrix element simulation script.
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r26435 | bugman | 2014-11-07 09:52:09 +0100 (Fri, 07 Nov 2014) | 3 lines

Simplification of some of the pseudo-ellipse 2nd degree frame order matrix equations.
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r26436 | bugman | 2014-11-07 10:08:53 +0100 (Fri, 07 Nov 2014) | 3 lines

More simplifications of the pseudo-ellipse 2nd degree frame order matrix equations.
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r26437 | bugman | 2014-11-07 10:11:47 +0100 (Fri, 07 Nov 2014) | 6 lines

Integer to float conversions in part_int_daeg2_pseudo_ellipse_13().

This avoid integer to float conversion during execution, saving a little time for the pseudo-ellipse
2nd degree frame order matrix compilation.
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r26438 | bugman | 2014-11-07 10:36:06 +0100 (Fri, 07 Nov 2014) | 3 lines

Removal of many repetitive calculations in the pseudo-ellipse 2nd degree frame order matrix equations.
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r26439 | bugman | 2014-11-07 10:39:17 +0100 (Fri, 07 Nov 2014) | 6 lines

Simplifications of pseudo-ellipse 1st degree frame order matrix functions.

The xx, yy, and zz have been renamed to 00, 11, and 22 for consistency. And all sigma_max arguments
have been dropped as they are not used.
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r26440 | bugman | 2014-11-07 11:44:51 +0100 (Fri, 07 Nov 2014) | 6 lines

Small numerical changes for the pseudo-ellipse 2nd degree frame order matrix graphs.

These are only for the first point close to zero and the changes are minimal, caused by the recent
simplifications of the code.
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r26441 | bugman | 2014-11-07 11:45:58 +0100 (Fri, 07 Nov 2014) | 6 lines

Created the Grace graphs for the free rotor pseudo-ellipse model 1st degree frame order matrix.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
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r26442 | bugman | 2014-11-07 13:46:13 +0100 (Fri, 07 Nov 2014) | 6 lines

Implemented the compile_1st_matrix_pseudo_ellipse_free_rotor() function.

This is for the lib.frame_order.pseudo_ellipse_free_rotor module. The function will calculate the
1st degree in-frame frame order matrix for the free_rotor pseudo-ellipse model.
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r26443 | bugman | 2014-11-07 14:16:04 +0100 (Fri, 07 Nov 2014) | 3 lines

Speed ups and simplifications of the free rotor pseudo-ellipse 2nd degree frame order matrix equations.
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r26444 | bugman | 2014-11-07 14:17:38 +0100 (Fri, 07 Nov 2014) | 3 lines

Added the torsionless isotropic cone model to the frame order matrix element simulation script.
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r26445 | bugman | 2014-11-07 15:10:57 +0100 (Fri, 07 Nov 2014) | 6 lines

Implemented the compile_1st_matrix_double_rotor() function.

This is for the lib.frame_order.double_rotor module. The function will calculate the 1st degree
frame order matrix for the double_rotor model.
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r26446 | bugman | 2014-11-07 15:11:37 +0100 (Fri, 07 Nov 2014) | 6 lines

Created the Grace graphs for the double rotor model 1st degree frame order matrix.

These are the values calculated directly from the lib.frame_order modules. The graphs were
previously all zeros.
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r26447 | bugman | 2014-11-07 15:46:33 +0100 (Fri, 07 Nov 2014) | 6 lines

Recreated all of the simulated pseudo-ellipse frame order matrix element graphs.

These are now in the Kronecker product notation so that they will match the graphs calculated using
the relax lib.frame_order.pseudo_ellipse module.
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r26448 | bugman | 2014-11-07 16:14:49 +0100 (Fri, 07 Nov 2014) | 3 lines

Fix for the pseudo-ellipse 1st degree frame order matrix Daeg22 element.
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r26449 | bugman | 2014-11-07 16:15:11 +0100 (Fri, 07 Nov 2014) | 3 lines

Updated all of the pseudo-ellipse 1st degree frame order matrix graphs for the recent fix.
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r26450 | bugman | 2014-11-07 16:44:37 +0100 (Fri, 07 Nov 2014) | 20 lines

Reverted r24463 as this is needed to conserve memory, especially for a large number of Sobol' points.

The command used was:
svn merge -r24463:r24462 .

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r24463 | bugman | 2014-07-05 19:06:09 +0200 (Sat, 05 Jul 2014) | 9 lines
Changed paths:
M /branches/frame_order_cleanup/target_functions/frame_order.py

Converted all frame order target function data structures to float64.

This affects the vector data structures used for the PCS numeric integration. The float32
structures added for speed do not actually increase the speed. For the double rotor model, 10
target function calls took the pcs_pivot_motion_double_rotor() function 44.936 seconds using float32
and 44.105 seconds using all float64. The cumulative time is also longer. This must be because
other parts are float64, and therefore type conversions are happening during target function calls.
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r26451 | bugman | 2014-11-07 16:51:22 +0100 (Fri, 07 Nov 2014) | 7 lines

Converted the Sobol' rotation matrices to float32 in the frame order target function.

This is to conserve huge amounts of memory to allow for more Sobol' points to be used. For example
for the models which use 3D Sobol' points (isotropic cone and pseudo-ellipse), a maximum of 50000
Sobol' points requires 50000000 to be created, using about 15 Gb of RAM.
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r26452 | bugman | 2014-11-07 17:18:52 +0100 (Fri, 07 Nov 2014) | 5 lines

A few Frame_order system test updates for the float64 to float32 memory saving changes.

The chi-squared value of 3 tests was slightly different.
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r26453 | bugman | 2014-11-07 18:19:46 +0100 (Fri, 07 Nov 2014) | 6 lines

Bug fix for the activation of quadratic integration in the frame order auto-analysis.

The calls to the frame_order.quad_int user function in the optimisation() method did not supply an
argument so the user function was defaulting to False rather than the True value required.
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r26454 | bugman | 2014-11-07 18:48:31 +0100 (Fri, 07 Nov 2014) | 5 lines

The frame order auto-analysis summary functions are now more robust.

If the data pipe already exists for some reason, it is deleted prior to the new one being created.
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r26455 | bugman | 2014-11-07 18:58:41 +0100 (Fri, 07 Nov 2014) | 6 lines

Changed the frame_order.quad_int user function argument default to True.

This means that calling the user function without arguments will activate the quadratic integration
rather than turning it off.
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r26456 | bugman | 2014-11-08 12:43:17 +0100 (Sat, 08 Nov 2014) | 3 lines

Added the isotropic cone model frame order matrix simulation graphs for the cone opening angle theta_x.
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r26457 | bugman | 2014-11-08 12:53:38 +0100 (Sat, 08 Nov 2014) | 3 lines

Created and added all of the torsionless isotropic cone simulated frame order matrix element graphs.
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r26458 | bugman | 2014-11-08 18:38:29 +0100 (Sat, 08 Nov 2014) | 7 lines

Added the free rotor isotropic cone model to the frame order matrix element simulation script.

The generated Grace graphs containing the matrix values for 1,000,000 simulation values have been
added to the repository. The self.torsion_check variable has been created to allow the
inside_iso_cone() method to skip the torsion angle check when its value is False.
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r26459 | bugman | 2014-11-09 10:45:14 +0100 (Sun, 09 Nov 2014) | 7 lines

Added the torsionless pseudo-ellipse model to the frame order matrix element simulation script.

The generated Grace graphs containing the matrix values for 1,000,000 simulation values have been
added to the repository. The rotations are generated by the rotation_hypersphere_torsionless()
method and the angle violations checked using the inside_pseudo_ellipse() method.
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r26460 | bugman | 2014-11-09 11:25:18 +0100 (Sun, 09 Nov 2014) | 5 lines

Bug fix for the torsionless pseudo-ellipse 1st degree frame order matrix.

The 11 element was of the wrong sign.
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r26461 | bugman | 2014-11-09 11:27:15 +0100 (Sun, 09 Nov 2014) | 3 lines

Fixes for the torsionless pseudo-ellipse 1st degree frame order matrix element graphs.
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r26462 | bugman | 2014-11-09 13:15:14 +0100 (Sun, 09 Nov 2014) | 8 lines

Recreated all of the simulated pseudo-ellipse frame order matrix element graphs.

These are now in the Kronecker product notation so that they will match the graphs calculated using
the relax lib.frame_order.pseudo_ellipse module.

The change of r26447 which should have recreated the graphs was incorrect.
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r26463 | bugman | 2014-11-09 13:28:18 +0100 (Sun, 09 Nov 2014) | 6 lines

Added the free rotor pseudo-ellipse model to the frame order matrix element simulation script.

This only required the self.torsion_check variable to be set to False. The model uses the
inside_pseudo_ellipse() and rotation_hypersphere() methods.
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r26464 | bugman | 2014-11-09 13:33:51 +0100 (Sun, 09 Nov 2014) | 5 lines

Fixes for free rotor isotropic cone 1st degree frame order matrix graphs calculated using relax.

The 1st degree function accepts the cone opening angle theta rather than the order parameter S.
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r26465 | bugman | 2014-11-09 16:43:24 +0100 (Sun, 09 Nov 2014) | 3 lines

Added the frame order matrix element graphs for the in-frame free rotor pseudo-ellipse model.
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r26466 | bugman | 2014-11-09 16:43:54 +0100 (Sun, 09 Nov 2014) | 3 lines

Added the frame order matrix element graphs for the out-of-frame free rotor pseudo-ellipse model.
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r26467 | bugman | 2014-11-09 17:39:59 +0100 (Sun, 09 Nov 2014) | 6 lines

Fixes for all of the calculated double rotor model frame order matrix graphs.

The X and Y angles were mixed up. The first torsion half-angle sigma1 corresponds to a y-axis
rotation and the second sigma2 corresponds to a x-axis rotation.
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r26468 | bugman | 2014-11-09 17:43:21 +0100 (Sun, 09 Nov 2014) | 6 lines

Reverted r26467 as too much was committed.

The command used was:
svn merge -r26467:r26466 .
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r26469 | bugman | 2014-11-09 17:47:14 +0100 (Sun, 09 Nov 2014) | 7 lines

Added support for the double rotor model to the frame order matrix element simulation script.

The double rotation is constructed in the new rotation_double_xy_axes() method, and the checks for
the violation of the two torsion angles in the inside_double_rotor() method. In the main loop, the
theta, phi and sigma angles correspond to sigma1, sigma2, and nothing.
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r26470 | bugman | 2014-11-09 17:48:05 +0100 (Sun, 09 Nov 2014) | 6 lines

Fixes for all of the calculated double rotor model frame order matrix graphs.

The X and Y angles were mixed up. The first torsion half-angle sigma1 corresponds to a y-axis
rotation and the second sigma2 corresponds to a x-axis rotation.
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r26471 | bugman | 2014-11-09 20:50:30 +0100 (Sun, 09 Nov 2014) | 3 lines

Added the frame order matrix element graphs for the double rotor model.
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r26472 | bugman | 2014-11-09 21:20:27 +0100 (Sun, 09 Nov 2014) | 5 lines

A divide by zero fix for the torsionless pseudo-ellipse.

This is in the compile_2nd_matrix_pseudo_ellipse_torsionless() relax library function.
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r26473 | bugman | 2014-11-09 21:22:29 +0100 (Sun, 09 Nov 2014) | 5 lines

A divide by zero fix for the free rotor pseudo-ellipse.

This is in the compile_2nd_matrix_pseudo_ellipse_free_rotor() relax library function.
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r26474 | bugman | 2014-11-09 22:23:54 +0100 (Sun, 09 Nov 2014) | 3 lines

Fix for r26460 - the second factor also needs to be inverted.
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r26475 | bugman | 2014-11-09 22:34:00 +0100 (Sun, 09 Nov 2014) | 7 lines

The 1st angle for the calculated frame order matrix graphs is 0 for all non pseudo-ellipse models.

This is for the frame_order_solution.py script. Only the pseudo-ellipse models where numerical
integration is required fail for the angle of 0.0. Therefore the changing of the first angle from
0.0 to 0.01 only occurs for the pseudo-ellipse models. All graphs have been updated.
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r26476 | bugman | 2014-11-09 22:45:24 +0100 (Sun, 09 Nov 2014) | 6 lines

The 1st pseudo-ellipse torsion angle value in the frame order matrix graphs is now 0.0.

Only the cone opening angles set to 0.0 cause a failure in the pseudo-ellipse models, so the torsion
angle is now allowed to start at exactly zero.
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r26477 | bugman | 2014-11-10 11:55:45 +0100 (Mon, 10 Nov 2014) | 3 lines

Clean up of the frame order matrix element simulation script.
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r26479 | bugman | 2014-11-10 14:27:50 +0100 (Mon, 10 Nov 2014) | 12 lines

Redesign of the free rotor isotropic cone frame order model - the order parameter has been replaced.

From the frame order matrix element graphs in test_suite/shared_data/frame_order/sim_vs_pred_matrix,
specifically Sijkl_iso_cone_free_rotor_in_frame_theta_x_calc.agr,
Sijkl_iso_cone_free_rotor_axis2_1_3_theta_x_calc.agr, and
Sijkl_iso_cone_free_rotor_out_of_frame_theta_x_calc.agr, it is clear that the symmetry of the order
parameter after 120 degrees causes the 2nd degree frame order matrix to be incorrectly estimated.
Therefore the S1 order parameter has been replaced with the original cone opening angle cone_theta.

All parts of relax have been updated for this large conversion.
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r26480 | bugman | 2014-11-10 14:30:00 +0100 (Mon, 10 Nov 2014) | 6 lines

Updated the frame order matrix element graphs for the free rotor isotropic cone fixes.

The cone S1 parameter has been converted back to the original cone theta opening half-angle,
allowing the 2nd degree frame order matrix elements to be properly calculated for all motions.
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r26481 | bugman | 2014-11-10 15:04:26 +0100 (Mon, 10 Nov 2014) | 8 lines

Eliminated the lib.frame_order.iso_cone.populate_*() functions.

The populate_1st_eigenframe_iso_cone() function was unused and incorrect, so it was deleted. The
contents of the populate_2nd_eigenframe_iso_cone() function have been shifted
compile_2nd_matrix_iso_cone() as a separate function is unnecessary. This now matches all the other
lib.frame_order modules.
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r26484 | bugman | 2014-11-10 16:16:54 +0100 (Mon, 10 Nov 2014) | 6 lines

Bug fix for the frame_order.simulate user function.

The incorrect model number was being specified and hence the simulation was not starting from the
optimised average domain position but rather the arbitrary position of the original structure.
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r26534 | bugman | 2014-11-11 16:41:51 +0100 (Tue, 11 Nov 2014) | 5 lines

Manual Python 3 fixes for the dict.key() function which returns a list or iterator in Python 2 or 3.

This matches r26519 in trunk.
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r26535 | bugman | 2014-11-11 16:51:21 +0100 (Tue, 11 Nov 2014) | 6 lines

Python 3 fixes via 2to3 - the "while 1" construct has been replaces with "while True".

The command used was:
2to3 -j 4 -w -f idioms .
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r26536 | bugman | 2014-11-11 17:28:08 +0100 (Tue, 11 Nov 2014) | 6 lines

Python 3 fixes via 2to3 - the spacing around commas has been fixed.

The command used was:
2to3 -j 4 -w -f ws_comma .
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r26537 | bugman | 2014-11-11 17:37:03 +0100 (Tue, 11 Nov 2014) | 6 lines

Python 3 fixes via 2to3 - the xrange() function has been replaced by range().

The command used was:
2to3 -j 4 -w -f xrange .
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r26657 | bugman | 2014-11-20 14:41:33 +0100 (Thu, 20 Nov 2014) | 5 lines

Started to create the Frame_order.test_pdb_model_rotor system test.

This will be used to check that the PDB representations of the frame order motions are correct.
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r26658 | bugman | 2014-11-20 14:46:04 +0100 (Thu, 20 Nov 2014) | 6 lines

Modified the frame_order.pdb_model user function backend to handle missing structural data.

The create_ave_pos() function of the specific_analyses.frame_order.geometric module now checks that
cdp.structure exists, and if not a warning is given and the PDB file creating is skipped.
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r26668 | bugman | 2014-11-20 16:14:01 +0100 (Thu, 20 Nov 2014) | 7 lines

Fixes for the frame_order.pdb_model user function backend for when no data is present.

The pipe_centre_of_mass() function of pipe_control.structure.mass module is now called with the
missing_error flag set to False so that the PDB generation can continue with the CoM set to [0, 0,
0].
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r26669 | bugman | 2014-11-20 16:15:13 +0100 (Thu, 20 Nov 2014) | 6 lines

The geometric representation part of the frame_order.pdb_model user function now checks parameters.

This calls the specific_analyses.frame_order.checks.check_parameters Check object to make sure that
all necessary parameters for the model exist.
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