relax SVN archive

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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Merged revisions 22071 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22071 | bugman | 2014-01-29 18:03:31 +0100 (Wed, 29 Jan 2014) | 5 lines

Created subsets of the CaM double rotor frame order test PCS data.

This consists of data for only 5 spins, and matches those of the other CaM frame order test data.
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Merged revisions 22070 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22070 | bugman | 2014-01-29 17:57:33 +0100 (Wed, 29 Jan 2014) | 5 lines

The CaM double rotor frame order test RDC data now has single quotes around the spin IDs.

This allows the data to be loaded in the Frame_order.test_cam_double_rotor system test.
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Merged revisions 22066-22067 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22066 | bugman | 2014-01-29 17:07:10 +0100 (Wed, 29 Jan 2014) | 5 lines

Fix for the Frame_order.test_generate_rotor2_distribution system test.

The rotation() method now must accept the motion_index keyword argument.
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r22067 | bugman | 2014-01-29 17:23:26 +0100 (Wed, 29 Jan 2014) | 5 lines

Created the Frame_order.test_cam_double_rotor system test for the CaM synthetic data.

This will be used to implement the frame order double rotor model.
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Merged revisions 22056-22064 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22056 | bugman | 2014-01-28 11:23:50 +0100 (Tue, 28 Jan 2014) | 7 lines

Fixes for the calculation of the frame order matrix in the test data generation base script.

The matrix generation now handles multiple modes of motion correctly. The total rotation matrix is
constructed when looping over the modes by using the dot product of the individual rotation to the
total, and then this is used to create the outer product, summed over all states.
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r22057 | bugman | 2014-01-28 11:24:33 +0100 (Tue, 28 Jan 2014) | 3 lines

Fix for the frame order test data generation base script for when the distribution of structures is not created.
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r22058 | bugman | 2014-01-28 11:25:13 +0100 (Tue, 28 Jan 2014) | 3 lines

The frame order test data generation base script now outputs the frame order matrix to 8 places.
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r22059 | bugman | 2014-01-28 11:30:02 +0100 (Tue, 28 Jan 2014) | 6 lines

Introduced the ROT_FILE flag to the frame order test data generation base script.

This allows the 'rotations.bz2' file creation to be skipped, if set to False. This file takes time
to create and is of limited use.
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r22060 | bugman | 2014-01-28 18:27:35 +0100 (Tue, 28 Jan 2014) | 3 lines

Removed a duplicated state.save call in the frame order test data generation base script.
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r22061 | bugman | 2014-01-29 09:08:33 +0100 (Wed, 29 Jan 2014) | 8 lines

The save file created by the frame order test data generation base script can now be bypassed.

When loading 1,000,000 PDB structures as models into the relax data store, the RAM usage can go over
10 Gb. When trying to save this into a relax state file with the state.save user function, the time
required can be over a day. Therefore the SAVE_STATE class variable has been introduced to allow
the state.save call to be bypassed.
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r22062 | bugman | 2014-01-29 11:33:18 +0100 (Wed, 29 Jan 2014) | 8 lines

Created the RDC and PCS back calculated test data for the CaM double rotor frame order model.

This consists of a uniform distribution over both rotors, the first centred in the C-domain and
the second in the N-domain, and the two axes being perpendicular to each other along the CoM-CoM
axis. The distribution consists of 250000 rotated structures. The frame order matrix for this
model is also given.
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r22063 | bugman | 2014-01-29 11:48:16 +0100 (Wed, 29 Jan 2014) | 7 lines

Created a distribution of structures for the CaM double rotor frame order model.

This is only for a distribution of 100 structures, to keep the file size to a reasonable size. A
PyMOL *.pse file is also included to show the distribution together with the rotor system and the
domain positions.
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r22064 | bugman | 2014-01-29 16:21:58 +0100 (Wed, 29 Jan 2014) | 6 lines

Updated for the rotation() method of all the CaM frame order test data generation scripts.

The motion_index argument is now accepted by all of the methods to allow the base script to execute
correctly.
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Merged revisions 22047-22048 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22047 | bugman | 2014-01-24 16:39:29 +0100 (Fri, 24 Jan 2014) | 7 lines

Created a simple double rotor geometric system to used for this frame order test data generation.

The system_create.py script creates the geometric system based on the CoMs of both domains in the
parent directory and two perpendicular rotation axes passing through both CoMs. A PDB file of the
representation is created by the script.
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r22048 | bugman | 2014-01-27 15:58:22 +0100 (Mon, 27 Jan 2014) | 8 lines

Improvements and expansion of the frame order test data generation base script.

More of the class variables are now defined in this base class and dummy methods are provided to
allow certain operations to be skipped (print_axis_system(), axes_to_pdb() and build_axes()).
Importantly, the script can now handle multiple modes of motion with the introduction of the key
_multi_system() and _state_loop() methods.
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Merged revisions 22039-22040 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22039 | bugman | 2014-01-21 11:43:21 +0100 (Tue, 21 Jan 2014) | 7 lines

Reintroduced the distribution PDB file creation to the frame order test data generation script.

This is the generate_base.py script in the test_suite/shared_data/frame_order/cam directory. The
ability to create the distribution.pdb file was long lost in this script, and can now be activated
using the DIST_PDB class variable.
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r22040 | bugman | 2014-01-22 11:19:22 +0100 (Wed, 22 Jan 2014) | 6 lines

The Frame Order test data generation base script now loads all structures before rotating them.

This allows the progress printout to function correctly by not having any user function printouts
as the rotations are occurring.
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