relax SVN archive

Merged revisions 25947,25957-25958 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25947 | bugman | 2014-09-22 11:15:17 +0200 (Mon, 22 Sep 2014) | 5 lines

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.
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r25957 | bugman | 2014-09-22 16:43:38 +0200 (Mon, 22 Sep 2014) | 6 lines

Modifications to the User_functions.test_structure_add_atom GUI test.

As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI
is now significantly different. Therefore many checks have been removed from the GUI test.
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r25958 | bugman | 2014-09-22 16:44:57 +0200 (Mon, 22 Sep 2014) | 6 lines

Added safety checks for NaN values to the lib.structure.pdb_write module.

This is within the _record_validate() function. The check prevents the creation of invalid PDB
files.
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Added safety checks for NaN values to the lib.structure.pdb_write module.

This is within the _record_validate() function. The check prevents the creation of invalid PDB
files.

Modifications to the User_functions.test_structure_add_atom GUI test.

As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI
is now significantly different. Therefore many checks have been removed from the GUI test.

Created the specific_analyses.frame_order.geometric.generate_axis_system() function.

This is now used by most parts of the frame order analysis to generate the full 3D eigenframe of the
motions. Previously this was implemented each time the frame or major axis was required. This
replicated and highly inconsistent code has been eliminated.

Changed the default PDB file name for the frame_order.simulate user function to 'simulate.pdb'.

The '*.bz2' extension has been dropped so that the file is quicker to create and does not need to be
decompressed for loading into molecular viewers.

Improvements for the frame_order.simulate user function.

The rigid model is now skipped, the PDB file closed, and some printouts for better user feedback
have been added.

Implemented the shifting to the average position for the frame_order.simulate user function backend.

This simply sends the structural object into the new average_position() function of the
specific_analyses.frame_order.geometric module.

Spun out the code for shifting to the average frame order position into a new function.

The old code of the create_ave_pos() of the specific_analyses.frame_order.geometric module has been
shifted into the new average_position() function. This will allow the code to be reused by other
parts of relax to obtain the average frame order structures.

Huge speed up for the Frame_order.test_auto_analysis user function.

The pseudo-Brownian dynamics simulation via the frame_order.simulate user function has been
massively speed up to allow the test to be almost as fast as before.

Added new arguments to the frame order auto-analysis for the frame_order.simulate user function.

These are the brownian_step_size, brownian_snapshot and brownian_total arguments which are passed
directly into the frame_order.simulate user function. This gives the user more control, as well as
allowing the test suite to speed up this part of the analysis.