relax SVN archive

Decreased the time required for the Frame_order.test_cam_* system tests.

The frame_order.simulate user function now only creates a total of 20 snapshots rather than 1000.

Created the backend framework for the frame_order.simulate user function.

The backend specific_analyses.frame_order.uf.simulate() function performs all data checks required,
prepares the output file object, assembles the frame order parameter values and pivot point, and
creates a copy of the structural object object with the ensemble collapsed into a single model.

All this data is then passed into the new lib.frame_order.simulation.brownian() function. This
initialises all required data structures and the structural object. The main loop of the simulation
is also implemented, taking snapshots at every fixed number of steps and terminating the loop once
the total number of snapshots are reached. The snapshot consists of copying the original unrotated
structural model and rotating it into the new position. The rotation is currently the identity
matrix.

The old specific_analyses.frame_order.geometric.create_distribution() stub function has been
deleted.

Created a basic text based progress meter in the new lib.text.progress module.

This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.

Merged revisions 25942-25945 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25942 | bugman | 2014-09-22 09:59:35 +0200 (Mon, 22 Sep 2014) | 6 lines

Created the Structure.test_collapse_ensemble system test.

This is used to test a planned feature of the internal structural object. The collapse_ensemble()
method will be created to remove all but one model in the structural ensemble.
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r25943 | bugman | 2014-09-22 10:14:25 +0200 (Mon, 22 Sep 2014) | 5 lines

Fixes for the structure.add_atom user function to allow for list of lists for the atomic position.

This allows different coordinates to be supplied for each model.
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r25944 | bugman | 2014-09-22 10:16:35 +0200 (Mon, 22 Sep 2014) | 5 lines

Modified the Structure.test_collapse_ensemble system test to check the initial values.

This is for sanity reasons as the test coverage of the structure.add_atom user function is poor.
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r25945 | bugman | 2014-09-22 10:29:55 +0200 (Mon, 22 Sep 2014) | 5 lines

Implemented the internal structural object collapse_ensemble() method.

This allows the Structure.test_collapse_ensemble system test to pass.
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Implemented the internal structural object collapse_ensemble() method.

This allows the Structure.test_collapse_ensemble system test to pass.

Modified the Structure.test_collapse_ensemble system test to check the initial values.

This is for sanity reasons as the test coverage of the structure.add_atom user function is poor.

Fixes for the structure.add_atom user function to allow for list of lists for the atomic position.

This allows different coordinates to be supplied for each model.

Created the Structure.test_collapse_ensemble system test.

This is used to test a planned feature of the internal structural object. The collapse_ensemble()
method will be created to remove all but one model in the structural ensemble.

Merged revisions 25923-25925,25927-25928,25933,25938-25940 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25923 | tlinnet | 2014-09-19 13:33:18 +0200 (Fri, 19 Sep 2014) | 3 lines

Implemented correlation plot of minimisation values.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25924 | bugman | 2014-09-19 17:24:51 +0200 (Fri, 19 Sep 2014) | 5 lines

Changed the missing package/module/software table in the test suite.

This is to allow all names to fit and to update the column titles for software packages.
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r25925 | bugman | 2014-09-19 17:38:48 +0200 (Fri, 19 Sep 2014) | 5 lines

Decreased the accuracy of a check in the Relax_disp.test_estimate_r2eff_err_auto system test.

This is to allow the test to pass on my Windows 7 VM.
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r25927 | bugman | 2014-09-19 18:29:51 +0200 (Fri, 19 Sep 2014) | 6 lines

Updated the frame order auto-analysis to call the new frame_order.simulate user function.

Although not implemented yet, this allows the user function to create the simulation PDB file in the
future.
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r25928 | bugman | 2014-09-19 18:32:38 +0200 (Fri, 19 Sep 2014) | 18 lines

Reverted r25927 as this should have been in the frame_order_cleanup branch, not the trunk!!!

The command used was:
svn merge -r25927:r25926 .

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r25927 | bugman | 2014-09-19 18:29:51 +0200 (Fri, 19 Sep 2014) | 6 lines
Changed paths:
M /trunk/auto_analyses/frame_order.py

Updated the frame order auto-analysis to call the new frame_order.simulate user function.

Although not implemented yet, this allows the user function to create the simulation PDB file in the
future.
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r25933 | bugman | 2014-09-20 10:15:36 +0200 (Sat, 20 Sep 2014) | 3 lines

Added Troels E. Linnet to the COMMITTERS file, which has not been updated in almost 3 years!
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r25938 | bugman | 2014-09-22 09:36:45 +0200 (Mon, 22 Sep 2014) | 6 lines

Created the Structure.test_get_model system test.

This demonstrates that the internal structural object get_model() method is not working as it
should.
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r25939 | bugman | 2014-09-22 09:39:29 +0200 (Mon, 22 Sep 2014) | 3 lines

Added a few more checks to the Structure.test_get_model system test.
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r25940 | bugman | 2014-09-22 09:40:11 +0200 (Mon, 22 Sep 2014) | 3 lines

Fix for the internal structural object get_model() method - it now actually returns the model.
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Fix for the internal structural object get_model() method - it now actually returns the model.