relax SVN archive

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.

Fix for inverted axes in the new Frame_order.test_pdb_model_rotor system test.

Merged revisions 26667,26670 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26667 | bugman | 2014-11-20 15:58:14 +0100 (Thu, 20 Nov 2014) | 9 lines

Big Python 3 bug fix for the dep_check module for the detection of the NMRPipe showApod software.

The showApod program was falsely detected as always not being present when using Python 3. This is
because the output of the program was being tested using string comparisons. However the output
from programs obtained from the subprocess module is no longer strings but rather byte-arrays in
Python 3. Therefore the byte-array is not being converted to text if Python 3 is being used,
allowing the showApod software to be detected.
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r26670 | bugman | 2014-11-20 16:39:20 +0100 (Thu, 20 Nov 2014) | 6 lines

Python 3 bug fix for the lib.spectrum.nmrpipe.show_apod_extract() function.

The subprocess module output from the showApod program, or any software, is a byte array in Python 3
rather than text. This is now detected and the byte array converted to text before any processing.
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Fixes for the unit tests of the lib.frame_order_matrix_ops module for the free rotor isotropic cone.

The S1 order parameter has been eliminated due to angles > pi/2.0 causing the frame order matrix to
be incorrectly predicted. Therefore all unit tests have been converted to use the cone opening
angle theta instead. In addition, the test_compile_2nd_matrix_iso_cone_free_rotor_disorder had been
modified to pass with the incorrect frame order matrix by comparing to the half cone frame order
matrix rather than the identity frame order matrix.

Merged revisions 26665 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26665 | bugman | 2014-11-20 15:43:52 +0100 (Thu, 20 Nov 2014) | 5 lines

Fix for the Structure.test_bug_22860_CoM_after_deletion system test for the previous commit.

The error is no longer RelaxNoPdbError but rather RelaxError.
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Completed the Frame_order.test_pdb_model_rotor system test.

This now sets the rotor axis to the z-axis (with a printout to be sure), sets the torsion angle to
zero for simplicity, creates a new data pipe and loads the PDB representation file, then checks all
of the key atom coordinates.

Python 3 bug fix for the lib.spectrum.nmrpipe.show_apod_extract() function.

The subprocess module output from the showApod program, or any software, is a byte array in Python 3
rather than text. This is now detected and the byte array converted to text before any processing.

The geometric representation part of the frame_order.pdb_model user function now checks parameters.

This calls the specific_analyses.frame_order.checks.check_parameters Check object to make sure that
all necessary parameters for the model exist.

Fixes for the frame_order.pdb_model user function backend for when no data is present.

The pipe_centre_of_mass() function of pipe_control.structure.mass module is now called with the
missing_error flag set to False so that the PDB generation can continue with the CoM set to [0, 0,
0].