relax SVN archive

Merged revisions 18590-18594 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18590 | bugman | 2013-03-01 23:44:16 +0100 (Fri, 01 Mar 2013) | 6 lines

Initialised a new package called 'lib'.

This will in the future be an extensive collection of functions, methods, classes, objects, etc.
useful for the study of all types of molecular dynamics.
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r18591 | bugman | 2013-03-01 23:46:56 +0100 (Fri, 01 Mar 2013) | 5 lines

Initialised the lib.geometry package.

This will be a library of all mathematics functions relating to geometry.
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r18592 | bugman | 2013-03-01 23:59:51 +0100 (Fri, 01 Mar 2013) | 3 lines

Added empty packages to the unit tests for the lib and lib.geometry packages.
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r18593 | bugman | 2013-03-02 00:04:48 +0100 (Sat, 02 Mar 2013) | 3 lines

Updated the maths_fns package __all__ list.
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r18594 | bugman | 2013-03-02 00:22:23 +0100 (Sat, 02 Mar 2013) | 3 lines

Updated the test_suite.unit_tests package __all__ list to be more modern.
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Added a small script to determine the combined rotations and translations of 1J7P_1st_NH_rot_trans.pdb.

This is compared to the original 1J7P_1st_NH.pdb file.

Created a PDB file which is a translation of 1J7P_1st_NH_rot.pdb by the vector [1, 2, 3].

This will be used for testing the optimisation of the translation parameters.

Fix for the full frame order analysis script in the test suite.

Added the verbosity argument to the generic_fns.structure.mass.centre_of_mass() function.

This allows the printouts to be turned off.

Updates for the full frame order analysis script in the test suite.

Initial attempt at allowing the average domain position to translate in the frame order analysis.

Previously only the domain orientation was optimised around a distant pivot point to achieve a
coupled translation and rotation. This was, however, an artifact of history from when only RDCs
were being used in the analysis. It should be possible to optimise both the translation and
orientation (independent of the pivot) of the moving domain.

For this, the frame_order.ave_pos_translation has been added to allow the translation optimisation
to be toggled. The parameters 'ave_pos_x', 'ave_pos_y' and 'ave_pos_z' have been added to the
model. The analysis specific code, auto-analysis, and target function code have been modified to
allow optimisation. However there are some issues and the translation optimisation does not work.
But the original code paths do function.

The calc user function for the frame order analysis now prints out the chi2 value.

Some small comment fixes in the specific_fns.frame_order module.

Removed some commented out dead code.