relax SVN archive

Implemented a method to automatically find dublicates of spectrum in exponential fit.

This is to ease the user intervention for error analysis, if this has been forgotten.

In the systemtest Relax_fit.test_curve_fitting_height_estimate_error(), moved the auto-detection of replicated spectra
into the manual method.

This is to prepare for auto-mated detection of replicates.

In the auto analysis of exponential fitting, changed the minimisation method from simplex to newton, to speed-up the fitting.

This is for master Monte-Carlo simulations.

Added systemtest Relax_fit.test_curve_fitting_height_estimate_error() for the manual and automated analysis of exponential fit.

This is to prepare for new methods in the auto analysis protocol.

Fix for the axis permutation protocol in the frame order auto-analysis.

This would fail if a results file for the permuted model already exists as the pipe.copy user
function call was being performed too early.

Simplified the optimisation in the axis permutation part of the frame order auto-analysis.

Only the last, highest quality setting is used for optimisation.

Modified the frame order auto-analysis.

The axis permutation algorithm is now performed on all isotopic cone and pseudo-ellipse models.
This is just in case the non-global minima was found in the original optimisation. The isotropic
cone models possess two local minima whereas the pseudo-ellipse models possess three local minima.

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/.

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy.

Created the other isotropic cone condition z <= x = y.

As there are no constraints in this model, this condition should not result in any major
differences, just the size of the cone being different and the optimisation having to decrease the
cone angle significantly to mimic the rotor.