relax SVN archive

Fix for systemtest Relax_disp.test_exp_fit(), where the spin.isotope was not set.

The new call to return_r2eff_arrays(), when producing graphs, raise RelaxSpinTypeError() if no isotope is set.

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.

Fix for interpolating time points, when producing xmgrace files for CPMG experiments.

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.

Fix for time not extracted for CPMG experiments in target_function-

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.

Fix to systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1()

After the relaxation times have been fixed, this model now return reasonable chi2 values.

The reported parameters are though quite different from all other models, and it seems something may
still be wrong.

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 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

........
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.