relax SVN archive

Merged revisions 22070 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
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.
........

Merged revisions 22066-22067 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
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.
........
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.
........

Merged revisions 22056-22064 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........

Merged revisions 22047-22048 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
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.
........
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.
........

Merged revisions 22039-22040 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
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.
........
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.
........

Merged revisions 22022-22023 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

........
r22022 | bugman | 2014-01-16 18:39:42 +0100 (Thu, 16 Jan 2014) | 3 lines

Created a directory for holding the CaM double rotor frame order synthetic data.
........
r22023 | bugman | 2014-01-17 09:40:42 +0100 (Fri, 17 Jan 2014) | 3 lines

Capitalised the pivot and CoM variables in the base frame order distribution generation script.
........

Initialized merge tracking via "svnmerge" with revisions "1-21950" from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

The centre of mass printout in the frame order target function setup now uses the verbosity argument.

This means that the printout is not shown for the Monte Carlo simulation optimisation.

Fixes for all of the CaM frame order optimisation scripts in the test data directories.

The frame_order.average_position user function is now essential.

Fixed a missing import.