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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.

bugman 2014-09-10

changed /branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Diff Switch to side-by-side view
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