relax SVN archive

Merged revisions 24788,24796-24797 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24788 | bugman | 2014-07-29 10:11:14 +0200 (Tue, 29 Jul 2014) | 9 lines

Implemented the pipe_control.mol_res_spin.format_info_full() function.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534.

This is a verbose representation of the spin information which can be used for presenting to the
user. Functions for shorter string versions will also be of great use, for example as described by
Troels at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6535.
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r24796 | bugman | 2014-07-29 10:25:37 +0200 (Tue, 29 Jul 2014) | 3 lines

Fix for the pipe_control.mol_res_spin.format_info_full() function, it now actually returns the string.
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r24797 | bugman | 2014-07-29 10:51:20 +0200 (Tue, 29 Jul 2014) | 5 lines

Created a unit test for the pipe_control.mol_res_spin.format_info_full() function.

This comprehensive test covers all input argument combinations.
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Missing import in the lib.frame_order.rotor module.

This was identified by the new Frame_order.test_auto_analysis system test.

Modified the optimisation of the rigid model in the frame order auto-analysis.

The grid search is now implemented as a zooming grid search.

Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests.

The base script now sets all parameter values so that the minimise.calculate user function can
operate. The two free rotor model chi-squared values have been updated as these are sensitive to
the motional eigenframe parameter values - these models can never approximate a rigid state.

Better handling of unset parameters in the frame order optimisation functions.

The specific_analyses.frame_order.optimisation.target_fn_data_setup() and
specific_analyses.frame_order.parameters.assemble_param_vector() function both now accept the
unset_fail argument. This is set in both the calculate() and minimise() API methods. When set, a
RelaxError will be raised in the assemble_param_vector() function when a parameter has not been set
yet. This together with previous changes will prevent the frame order analysis from using 0.0 as a
starting value for unset parameters.

Renamed the other return grace data function, to a better shorter name.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Renamed return grace data function, to a better shorter name.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Made the plotting function uniform into accepting both CPMG and R1rho data.

Also made a function to return data, depending if it is data, back calculated, interpolated or residual.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Modified the specific_analyses.frame_order.parameters.assemble_param_vector() function.

This can now handle the case of no parameters being present. The corresponding elements of the
numpy array will consist of NaN values.

Modified the specific_analyses.frame_order.parameters.update_model() function.

This will no longer set all parameters to 0.0, excluding the pivot point.