relax SVN archive

Bug fix for the new frame_order.permute_axes user function.

The cone and torsion angles were not being correctly permuted. Now the direct permutation array is
being used. And the fact that cone_theta_x is a rotation along the y-axis and cone_theta_y along
the x-axis is taken into account.

Created some test data files for visualising the frame order axis permutation.

This uses the CaM frame order synthetic data for the rotor model to visualise the pseudo-ellipse
frame order model axis permutations. The initial conversion sets the pseudo-ellipse torsion angle
cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic cone opening to close to
zero. Then the axis permutations are performed. All three solutions are optimised. PDB
representations before and after optimisation are included to illustrate any problems.

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

The pipe.copy user function does not switch pipes, therefore the pipe.switch user function is now
being called so that the correct pipe is being permuted and optimised.

Many fixes for the frame_order.permute_axes user function.

The z-axis inversion is now encoded into a 3D numpy array as the index of the new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be reintroduced later).

Fix for the Frame_order.test_axis_perm_x_le_z_le_y_permB system test.

The permuted z-axis needs to be inverted in the test.

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.