relax SVN archive

Created a number of system tests to check the diffusion tensor PDB representation.

This is to prevent bugs such as #22502 (https://gna.org/bugs/?22502) from ever reappearing. The PDB
file contents are hardcoded into the tests and checked. The tests include
Structure.test_create_diff_tensor_pdb_ellipsoid, Structure.test_create_diff_tensor_pdb_oblate,
Structure.test_create_diff_tensor_pdb_prolate, and Structure.test_create_diff_tensor_pdb_sphere.

Merged revisions 25208-25209 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25208 | bugman | 2014-08-22 12:32:52 +0200 (Fri, 22 Aug 2014) | 5 lines

Updated the diffusion tensor PDB representation files.

This replaces the broken prolate representation with the corrected representation.
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r25209 | bugman | 2014-08-22 12:34:41 +0200 (Fri, 22 Aug 2014) | 3 lines

Deleted the duplicated Structure.test_create_diff_tensor_pdb system test.
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Deleted the duplicated Structure.test_create_diff_tensor_pdb system test.

Updated the diffusion tensor PDB representation files.

This replaces the broken prolate representation with the corrected representation.

Merged revisions 25206 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25206 | bugman | 2014-08-22 12:08:09 +0200 (Fri, 22 Aug 2014) | 9 lines

Fix for bug #22502 (https://gna.org/bugs/?22502).

This is the problem whereby the geometric prolate diffusion representation does not align with axis
in PDB, as reported by Martin Ballaschk (https://gna.org/users/mab).

This problem was not the main prolate tensor axis, but that the geometric object needed to be
rotated 90 degrees about the z-axis to bring the object and axis into the same frame.
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Fix for bug #22502 (https://gna.org/bugs/?22502).

This is the problem whereby the geometric prolate diffusion representation does not align with axis
in PDB, as reported by Martin Ballaschk (https://gna.org/users/mab).

This problem was not the main prolate tensor axis, but that the geometric object needed to be
rotated 90 degrees about the z-axis to bring the object and axis into the same frame.

Merged revisions 25204 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25204 | bugman | 2014-08-22 11:55:21 +0200 (Fri, 22 Aug 2014) | 12 lines

Added an optimisation script for the test_suite/shared_data/diffusion_tensor/ellipsoid relaxation data.

This is to help catch bug #22502 (https://gna.org/bugs/?22502), the geometric prolate diffusion
representation does not align with axis in PDB, as reported by Martin Ballaschk
(https://gna.org/users/mab).

The PDB files of the optimised tensor demonstrate exactly the same problem as seen in the files
attached to the bug report. The oblate and spherical diffusion tensor representations match that of
the ellipsoid. But the prolate axis and tensor orientation are both different from the ellipsoid
as well as themselves.
........

Added an optimisation script for the test_suite/shared_data/diffusion_tensor/ellipsoid relaxation data.

This is to help catch bug #22502 (https://gna.org/bugs/?22502), the geometric prolate diffusion
representation does not align with axis in PDB, as reported by Martin Ballaschk
(https://gna.org/users/mab).

The PDB files of the optimised tensor demonstrate exactly the same problem as seen in the files
attached to the bug report. The oblate and spherical diffusion tensor representations match that of
the ellipsoid. But the prolate axis and tensor orientation are both different from the ellipsoid
as well as themselves.

Merged revisions 25202 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25202 | bugman | 2014-08-22 11:28:35 +0200 (Fri, 22 Aug 2014) | 7 lines

Another fix for bug #22505 (https://gna.org/bugs/?22505).

This is the failure of the structure.create_diff_tensor_pdb user function when no structural data is
present. Now the cdp.structure data structure is checked, when present, if it contains any data
using its own empty() method.
........

Another fix for bug #22505 (https://gna.org/bugs/?22505).

This is the failure of the structure.create_diff_tensor_pdb user function when no structural data is
present. Now the cdp.structure data structure is checked, when present, if it contains any data
using its own empty() method.