relax SVN archive

Reverted r24827 as this was two commits mixed up.

The command used was:
svn merge -r24827:r24826 .

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r24827 | tlinnet | 2014-07-30 12:53:04 +0200 (Wed, 30 Jul 2014) | 4 lines

Fix for output catching after re-order or return_offset_data() function.

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].
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Fix for output catching after re-order or return_offset_data() function.

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].

Removed unused plotting function.

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 plotting function to represent the function of writing to file.

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].

Hardcoded xmgrace colour_order, and made function to return data label, and data plot settings, depending on data type.

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].

Added linear constraints for the pivot and average domain translation frame order parameters.

The pivot coordinates are constrained between -999 and 999 Angstrom and the translation between -500
and 500 Angstrom. This allows the frame_order.pdb_model user function to operate in the case of
failed models - often the free rotors fitting to torsionally restricted data - by preventing the PDB
coordinates from being out of the PDB format range. It should also speed up optimisation by
stopping the optimisation of failed models earlier.

Implementation of the Optimisation_settings object in the frame order auto-analysis.

This object holds all of the grid search, zooming grid search, and minimisation settings. It
provides the add_grid() and add_min() methods to allow the user to add successive iterations of
optimisation and settings to the object. The loop_grid() and loop_min() methods are used to loop
over each iteration of each method. And the get_grid_inc(), get_grid_num_int_pts(),
get_grid_zoom_level(), get_min_algor(), get_min_func_tol() and get_min_num_int_pts() methods are
used to access the user defined settings.

The auto-analysis has been redesigned around this new concept. All of the optimisation arguments
have been replaced. Instead there are the opt_rigid, opt_subset, opt_full, and opt_mc arguments
which are expected to be instances of the Optimisation_settings object. The optimisation in the
auto-analysis is now more advanced in that more user optimisation settings are now available and
active.

Redesigned the Frame_order.test_auto_analysis system test.

This now uses a hypothetical new Optimisation_settings object from the frame order auto-analysis
module for holding all of the grid search, zooming grid search and minimisation settings. This will
allow for far greater user control of the settings and hugely simplify the auto-analysis interface
by decreasing the number of input arguments. It should also be less confusing.

Updates and fixes for the frame order auto-analysis.

The custom grid setup now works for the new reduced parameter set models and the double rotor model
is now also included. The cone axis alpha angle to spherical angle conversion has had a bug
removed. And some of the printouts are now more detailed.

Missing import in the lib.frame_order.double_rotor module.

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