relax SVN archive

Merged revisions 22176-22178,22192-22194 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22176 | bugman | 2014-02-12 14:56:21 +0100 (Wed, 12 Feb 2014) | 7 lines

Changes to the frame_order.pivot user function.

The 'order' argument has been added to allow for multiple pivots to be present. The user function
backend will store these as cdp.pivot, cdp.pivot2, cdp.pivot3, etc. The 'fix' argument is now
defaulting to False to make sure it is always boolean.
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r22177 | bugman | 2014-02-12 16:20:38 +0100 (Wed, 12 Feb 2014) | 3 lines

The second pivot is now being passed into the frame order target function class.
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r22178 | bugman | 2014-02-13 09:55:09 +0100 (Thu, 13 Feb 2014) | 6 lines

Simplified the CaM frame order system test base script.

The class variables are now always defined, so checking for their existence is pointless. The
CONE_S1 is now also defined in the base script as a class variable.
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r22192 | bugman | 2014-02-14 17:25:00 +0100 (Fri, 14 Feb 2014) | 10 lines

Converted the Frame_order.test_cam_rotor system script test to use the new rotor model parameters.

The rotor frame order parameters {P_alpha, P_beta, P_gamma, T_x, T_y, T_z, E_theta, E_phi, p_x, p_y,
p_z}, where P_i are the Euler angles defining the average domain position, T_i are the translations
defining the average domain position, E_i are the Eigenframe angles defining the rotation axis, and
p_i are the pivot point coordinates, will be converted to {P_alpha, P_beta, P_gamma, T_x, T_y, T_z,
Ax_alpha, p_x, p_y, p_z}. Ax_alpha is the new parameter which defines the rotation axis together
with the pivot using the minimal parameter set {p_x, p_y, p_z, Ax_alpha}.
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r22193 | bugman | 2014-02-14 17:26:33 +0100 (Fri, 14 Feb 2014) | 3 lines

Added support for the new axis_alpha frame order parameter to the specific_analyses.frame_order package.
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r22194 | bugman | 2014-02-14 17:54:31 +0100 (Fri, 14 Feb 2014) | 6 lines

Implemented the new frame order rotor model parameters in the target function.

The parameters {axis_theta, axis_phi} have been replaced by the single axis_alpha. To support the
new model construct, the CoM of the entire system is now passed into the target function.
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Merged revisions 22171-22175 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22171 | bugman | 2014-02-12 09:30:17 +0100 (Wed, 12 Feb 2014) | 3 lines

Capitalised the class variables of all of the CaM frame order system test scripts.
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r22172 | bugman | 2014-02-12 10:14:05 +0100 (Wed, 12 Feb 2014) | 6 lines

Class variable cleanup for the CaM frame order system test scripts.

The variables are now all defined in the base script and only overwritten when needed by the
individual tests.
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r22173 | bugman | 2014-02-12 10:16:47 +0100 (Wed, 12 Feb 2014) | 3 lines

Updated the test_suite.system_tests.scripts.frame_order.cam package __all__ list.
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r22174 | bugman | 2014-02-12 11:14:09 +0100 (Wed, 12 Feb 2014) | 6 lines

Changed the handling of the pivot point in the CaM frame order system tests.

The pivot point is now a class variable, rather than being hardcoded into a function. The handling
of a second pivot has also been added.
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r22175 | bugman | 2014-02-12 11:15:07 +0100 (Wed, 12 Feb 2014) | 3 lines

Updated the CaM frame order double rotor system test script to have the correct two pivots.
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Merged revisions 22170 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22170 | bugman | 2014-02-12 09:13:08 +0100 (Wed, 12 Feb 2014) | 3 lines

Added a simple script for analysing the Eigensystem of the CaM frame order double rotor test model.
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Merged revisions 22169 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22169 | bugman | 2014-02-10 17:48:18 +0100 (Mon, 10 Feb 2014) | 3 lines

Import fix for the changes to the specific_analyses.frame_order package layout.
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Merged revisions 22140-22142 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22140 | bugman | 2014-02-07 08:51:59 +0100 (Fri, 07 Feb 2014) | 6 lines

The double rotor system is now truly perpendicular.

This is for the CaM frame order synthetic test data. The two axes were not perpendicular whereas
for the model they should be.
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r22141 | bugman | 2014-02-07 09:04:11 +0100 (Fri, 07 Feb 2014) | 6 lines

Updated the double rotor distribution PDB file for the perpendicular axes.

This is for the CaM frame order double rotor synthetic data. The number of structures in this
distribution is set to 100 (10 per motional mode). The PyMOL *.pse file has also been updated.
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r22142 | bugman | 2014-02-07 10:44:54 +0100 (Fri, 07 Feb 2014) | 6 lines

Updated the CaM frame order double rotor synthetic test data for the perpendicular axes.

The RDC and PCS data has been recalculated for 250,000 structures, this time with the axes being
truly perpendicular.
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Merged revisions 22114 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22114 | bugman | 2014-02-04 10:24:23 +0100 (Tue, 04 Feb 2014) | 7 lines

Changed the precision of the deactivated Frame_order.test_cam_double_rotor_pcs system test.

This test will run with the command "relax -s Frame_order.test_cam_double_rotor_pcs" and, because of
the small angle of the test model, the chi-squared value differences for just the PCS were too small
for the previous precision of 1 decimal place.
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Merged revisions 22109-22112 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22109 | bugman | 2014-02-03 12:36:46 +0100 (Mon, 03 Feb 2014) | 3 lines

Copyright notice update.
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r22110 | bugman | 2014-02-03 13:35:23 +0100 (Mon, 03 Feb 2014) | 7 lines

Initial implementation of the lib.frame_order.double_rotor module.

This module implements the functions needed to solve the frame order analysis for the RDC (via the
frame order matrix) and PCS (numerically). The interfaces have been updated for the double rotor
but most of the code still implements the basic rotor model from which it derives.
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r22111 | bugman | 2014-02-03 15:14:22 +0100 (Mon, 03 Feb 2014) | 5 lines

Fix for the double rotor frame order model when only RDCs are used.

The target function was not being aliased when no PCS data was present.
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r22112 | bugman | 2014-02-03 15:26:28 +0100 (Mon, 03 Feb 2014) | 3 lines

Removal of unused imports from the lib.frame_order.double_rotor module.
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Merged revisions 22106-22107 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22106 | bugman | 2014-01-31 17:26:59 +0100 (Fri, 31 Jan 2014) | 3 lines

Better support for the parameters of the double rotor frame order model.
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r22107 | bugman | 2014-01-31 17:32:20 +0100 (Fri, 31 Jan 2014) | 7 lines

Initial implementation of the double rotor frame order model target function.

The target function func_double_rotor() has been created as a copy of the func_rotor_qrint() method,
modified for the double rotor model. Modifications will likely be needed as the
compile_2nd_matrix_double_rotor() and pcs_numeric_int_double_rotor() functions are implemented.
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Merged revisions 22073 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22073 | bugman | 2014-01-30 14:36:43 +0100 (Thu, 30 Jan 2014) | 3 lines

Added the double rotor frame order model to the frame_order.select_model user function.
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Merged revisions 22072 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22072 | bugman | 2014-01-30 11:03:05 +0100 (Thu, 30 Jan 2014) | 8 lines

Large refactorisation of the frame order package.

The private methods of the frame order package specific_analyses.frame_order have now all been
shifted into modules. This is to simplify the package by not having huge quantities of code in the
__init__ module. Now the code resides in the api, checks, data, optimisation, parameters, and
user_functions modules.
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