relax SVN archive

Modified target function of relax disp, to use the the new list of time points, which are of higher dimension.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Modified back_calc_r2eff() to accept interpolated timepoints.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Modified following functions:

Time points are now saved at the [ei][mi][oi][di] index level.
At this index Ãlevelall time points are saved for the R2eff point.

- interpolate_disp()
To interpolate time points, all time points through the original dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- interpolate_offset()
To interpolate time points, all time points through the original offset points, and then dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- plot_disp_curves_to_file()
To acquire the original relax_times points.

- return_r2eff_arrays()
To save all time points on the level of [ei][mi][oi][di].
At this index level, it will be a numpy array list with all time values used for fitting.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Improved data checking for all of the Structure system tests.

Before looping over the structural data, the number of lines in the real file and the newly
generated file are compared. This avoids the situation whereby an empty file is produced,
accidentally allowing the test to pass.

Merged revisions 25211 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25211 | bugman | 2014-08-22 14:05:34 +0200 (Fri, 22 Aug 2014) | 8 lines

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.
........

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.
........