relax SVN archive

Created 6 system tests for the frame_order.permute_axes user function.

This covers the 3 starting conditions (x<y<z, x<z<y, z<x<y) and the two permutations ('A' and 'B')
for each of these which do not include the starting permutation. They replace the original
Frame_order.test_axis_permutation system test with the tests
Frame_order.test_axis_perm_x_le_y_le_z_permA, Frame_order.test_axis_perm_x_le_y_le_z_permB,
Frame_order.test_axis_perm_x_le_z_le_y_permA, Frame_order.test_axis_perm_x_le_z_le_y_permB,
Frame_order.test_axis_perm_z_le_x_le_y_permA, and Frame_order.test_axis_perm_z_le_x_le_y_permB.

Redesigned the frame_order.permute_axes user function frontend.

Previously only cyclic permutations were considered, however non-cyclic permutations are also
allowed when accompanied by an axis inversion. Therefore 3 combinations exist with cone_theta_x <=
cone_theta_y, or 2 when the current combination is excluded.

Added extensive printouts to the frame_order.permute_axes user function.

The axis permutation step in the frame order auto-analysis is now always performed.

If an old results file was found, this step was accidentally skipped.

Made the pivot point in the frame order PDB representation fail-proof.

If the pivot position was outside of the bounds [-1000, 1000], the PDB file creation would fail as
the record would be too long. So now the pivot is shifted to be in these bounds.

Merged revisions 25709,25712,25716-25719 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25709 | tlinnet | 2014-09-08 22:23:07 +0200 (Mon, 08 Sep 2014) | 3 lines

Initial try to implement plotting in the repeated auto analysis protocol.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25712 | tlinnet | 2014-09-09 13:00:39 +0200 (Tue, 09 Sep 2014) | 3 lines

Small improvement of the matplotlib plotting of data in the repeated analysis protocol.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25716 | tlinnet | 2014-09-09 15:07:34 +0200 (Tue, 09 Sep 2014) | 3 lines

Fix for calling correct folder with test intensities.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25717 | tlinnet | 2014-09-09 15:07:37 +0200 (Tue, 09 Sep 2014) | 4 lines

Fix for two-point calculatation of exponential curve with corrupted data.

The two-point calculatation calculation is now also skipped, if the measured intensity is 0.
This can happen for corrupted intensity files.
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r25718 | tlinnet | 2014-09-09 18:18:11 +0200 (Tue, 09 Sep 2014) | 3 lines

For the class of repeated analysis, implemented method to collect peak intensity, and function to plot the correlation.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25719 | tlinnet | 2014-09-09 18:18:13 +0200 (Tue, 09 Sep 2014) | 3 lines

Added systemtest Relax_disp.test_repeat_cpmg to be skipped, if no matplotlib module exists.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Fix for the reading of old results files in the frame order auto-analysis.

The directory name is now processed by the model_directory() method. This will convert the spaces
to '_' and remove commas. Without this the already created files could not be found, if the model
name contains a space or comma.

Added support for axis permutations in the frame order auto-analysis.

This is done by copying the data pipe of the already optimised pseudo-elliptic models, permuting the
axes, and performing another optimisation using all RDC and PCS data. This allows the second
solution for these pseudo-elliptic models to be found. The 2nd pipe is included in the model
selection step to allow the best solution for the model to be found.

Fix for the frame_order.permute_axes user function for the torsionless pseudo-ellipse.

This should have been part of the last commit.

The frame_order.permute_axes user function can now handle the torsionless pseudo-ellipse.

This model does not have the variable cdp.cone_sigma_max set.