relax SVN archive

Modified the frame order auto-analysis axis permutation algorithm to handle both permutations.

Instead of creating one additional data pipe for the permutations, two are now created for the
permutations 'A' and 'B'. This allows all 3 solutions for the pseudo-elliptic models to be
explored and included in the final model selection process.

Fix for the frame_order.permute_axes for the torsionless pseudo-ellipse model.

The data structure cdp.cone_sigma_max does not exist in this model as cone_sigma_max == 0.0.

Removed the second permutation from the 6 Frame_order.test_axis_perm_* system tests.

A second identical permutation does not necessarily restore the original state.

Implemented the new frame_order.permute_axes backend.

The 3 starting conditions x<y<z, x<z<y, and z<x<y and the two permutations 'A' and 'B' (for each of
these which do not include the starting permutation) are now supported. For these 6 combinations,
the axis and order parameter permutation and the z-axis inversion are selected and applied to the
current system.

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

........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........