relax SVN archive

Small fix for the Frame_order.test_pdb_model_iso_cone system test for the 'B' representation.

Fix for the cone sized created by the frame_order.pdb_model user function.

The 'size' argument was not being used at all for the cone size. It is now passed into the
lib.structure.represent.cone.cone() function as the 'scale' argument.

Created the Frame_order.test_pdb_model_iso_cone system test.

This is for checking the PDB representation of the isotropic cone frame order model created by the
frame_order.pdb_model user function. It checks both A and B representations.

Merged revisions 26679,26681 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26679 | bugman | 2014-11-21 10:12:42 +0100 (Fri, 21 Nov 2014) | 3 lines

Fix for the unit tests to match r26656 - Python 2.5 floats do not have a 'real' property.
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r26681 | bugman | 2014-11-21 10:29:34 +0100 (Fri, 21 Nov 2014) | 9 lines

Bug fix for the lib.structure.angles.angles_*() functions for odd increments.

This affects the PDB representations of the diffusion tensor and frame order when the number of
increments in the respective user functions is set to an odd number. It really only affects the
frame_order.pdb_model user functions, as the number of increments cannot be set in any of the other
user functions (structure.create_diff_tensor_pdb, structure.create_rotor_pdb,
structure.create_vector_dist, n_state_model.cone_pdb).
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Bug fix for the lib.structure.angles.angles_*() functions for odd increments.

This affects the PDB representations of the diffusion tensor and frame order when the number of
increments in the respective user functions is set to an odd number. It really only affects the
frame_order.pdb_model user functions, as the number of increments cannot be set in any of the other
user functions (structure.create_diff_tensor_pdb, structure.create_rotor_pdb,
structure.create_vector_dist, n_state_model.cone_pdb).

Simplification of the Frame_order.test_pdb_model_rotor system test.

The size is now programatically handled.

Fix for the unit tests to match r26656 - Python 2.5 floats do not have a 'real' property.

Created the Frame_order.test_pdb_model_rotor2 system test to check for an offset pivot.

The pivot is set to [1, 0, 1] so that the rotor axis is tilted -45 degrees in the xz-plane. And the
size of the geometric object is set to 100 Angstrom for better testing of the sizes of the elements.

Size fix for the rotor representation from the frame_order.pdb_model user function.

The size problem was detected via the Frame_order.test_pdb_model_rotor system test. The rotors in
the PDB representation were all fixed in size, and ignored the 'size' argument of the
frame_order.pdb_model user function. The size argument is now passed into the add_rotors() function
of the specific_analyses.frame_order.geometric and passed on to the rotor() function of the
lib.structure.represent.rotor module.

Huge bug fix for the frame_order.pdb_model user function - the single axis direction was incorrect.

In the PDB representation of the frame order motion for the rotor and isotropic cone models (rotor,
free rotor, isotropic cone, free rotor isotropic cone, and torsionless isotropic cone), the X and Z
axes were swapped. This is because the eigenframe of the motion was being incorrectly constructed
via the lib.geometry.rotations.two_vect_to_R() function.

For better control, the specific_analyses.frame_order.geometric.frame_from_axis() function has been
created. This constructs a full motional eigenframe from the Z-axis. The problem was detected via
the new Frame_order.test_pdb_model_rotor system test.