relax SVN archive

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].

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.

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.
........

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.

Merged revisions 26662 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26662 | bugman | 2014-11-20 15:27:47 +0100 (Thu, 20 Nov 2014) | 7 lines

Added the missing_error keyword argument to the pipe_centre_of_mass() function.

This is from the pipe_control.structure.mass module. The new keyword controls what happens with the
absence of structural data. The pipe_control.structure.checks.check_structure() function is now
being used to either throw a warning and return [0, 0, 0] or to raise a RelaxError.
........

Merged revisions 26662 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26662 | bugman | 2014-11-20 15:27:47 +0100 (Thu, 20 Nov 2014) | 7 lines

Added the missing_error keyword argument to the pipe_centre_of_mass() function.

This is from the pipe_control.structure.mass module. The new keyword controls what happens with the
absence of structural data. The pipe_control.structure.checks.check_structure() function is now
being used to either throw a warning and return [0, 0, 0] or to raise a RelaxError.
........

Added the missing_error keyword argument to the pipe_centre_of_mass() function.

This is from the pipe_control.structure.mass module. The new keyword controls what happens with the
absence of structural data. The pipe_control.structure.checks.check_structure() function is now
being used to either throw a warning and return [0, 0, 0] or to raise a RelaxError.