relax SVN archive

Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to match the data.

Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.

If the second atom of the pair in the intermolecular data container holding the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second
atoms being pseudo-atoms is supported.

Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.

This is a test of the long range, absolute RDCs for menthol.

Fixes for the frame order system tests on Mac OS X.

The numerical precision on a Mac is quite different, and this has a dramatic effect on the optimised
chi-squared value. The precision is only to about 1 decimal place!

Merged revisions 18028,18031-18032 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18028 | bugman | 2012-11-23 16:34:37 +0100 (Fri, 23 Nov 2012) | 3 lines

The rdc.write and pcs.write user functions now skip deselected spins.
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r18031 | bugman | 2012-11-26 12:21:05 +0100 (Mon, 26 Nov 2012) | 6 lines

The axis for PDB geometric cone can now be turned off in the create_cone_pdb() function.

The axis_flag keyword argument is now accepted and if False will cause the axis to be excluded.
This is useful for the frame order cones for example as its own {x,y,z}-axis system is created.
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r18032 | bugman | 2012-11-26 12:24:45 +0100 (Mon, 26 Nov 2012) | 3 lines

Many docstring fixes for the functions of the generic_fns.structure.geometric module.
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Merged revisions 18028,18031-18032 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18028 | bugman | 2012-11-23 16:34:37 +0100 (Fri, 23 Nov 2012) | 3 lines

The rdc.write and pcs.write user functions now skip deselected spins.
........
r18031 | bugman | 2012-11-26 12:21:05 +0100 (Mon, 26 Nov 2012) | 6 lines

The axis for PDB geometric cone can now be turned off in the create_cone_pdb() function.

The axis_flag keyword argument is now accepted and if False will cause the axis to be excluded.
This is useful for the frame order cones for example as its own {x,y,z}-axis system is created.
........
r18032 | bugman | 2012-11-26 12:24:45 +0100 (Mon, 26 Nov 2012) | 3 lines

Many docstring fixes for the functions of the generic_fns.structure.geometric module.
........

Merged revisions 18028,18031-18032 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18028 | bugman | 2012-11-23 16:34:37 +0100 (Fri, 23 Nov 2012) | 3 lines

The rdc.write and pcs.write user functions now skip deselected spins.
........
r18031 | bugman | 2012-11-26 12:21:05 +0100 (Mon, 26 Nov 2012) | 6 lines

The axis for PDB geometric cone can now be turned off in the create_cone_pdb() function.

The axis_flag keyword argument is now accepted and if False will cause the axis to be excluded.
This is useful for the frame order cones for example as its own {x,y,z}-axis system is created.
........
r18032 | bugman | 2012-11-26 12:24:45 +0100 (Mon, 26 Nov 2012) | 3 lines

Many docstring fixes for the functions of the generic_fns.structure.geometric module.
........

Added symbolic links for all of the CaM frame order test models to the full_analysis.py script.

Added some comments showing what the angles are in radians.

This is for the CaM pseudo-ellipse frame order test data optimisation script.

The angles of the cone axis for the frame order eigenframe are now wrapped between 0 and 2pi.

This is needed for the numerical stability of the trigonometric functions, and for better
visualisation.