relax SVN archive

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.
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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

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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.
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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.

Merged revisions 26656,26659 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26656 | bugman | 2014-11-20 14:40:42 +0100 (Thu, 20 Nov 2014) | 6 lines

Python 2.5 fix for the align_tensor.display user function.

The new irreducible spherical tensor coefficient printout was failing as the float.real variable was
introduced from Python 2.6 onwards.
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r26659 | bugman | 2014-11-20 15:05:32 +0100 (Thu, 20 Nov 2014) | 7 lines

Shifted the structure checks into their own module.

This shifts the special check_structure Check object from pipe_control.structure.main into the new
checks module. It allows the check to be performed by other modules in the pipe_control.structure
package.
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Merged revisions 26656,26659 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26656 | bugman | 2014-11-20 14:40:42 +0100 (Thu, 20 Nov 2014) | 6 lines

Python 2.5 fix for the align_tensor.display user function.

The new irreducible spherical tensor coefficient printout was failing as the float.real variable was
introduced from Python 2.6 onwards.
........
r26659 | bugman | 2014-11-20 15:05:32 +0100 (Thu, 20 Nov 2014) | 7 lines

Shifted the structure checks into their own module.

This shifts the special check_structure Check object from pipe_control.structure.main into the new
checks module. It allows the check to be performed by other modules in the pipe_control.structure
package.
........

Shifted the structure checks into their own module.

This shifts the special check_structure Check object from pipe_control.structure.main into the new
checks module. It allows the check to be performed by other modules in the pipe_control.structure
package.

Modified the frame_order.pdb_model user function backend to handle missing structural data.

The create_ave_pos() function of the specific_analyses.frame_order.geometric module now checks that
cdp.structure exists, and if not a warning is given and the PDB file creating is skipped.