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Relax 3.3.0

24 bytes added, 08:47, 16 October 2020
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* Created the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb Structure.test_create_diff_tensor_pdb system test]. This is to show the failure of the [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb user function] when no structural data is present.
* Created the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb2 Structure.test_create_diff_tensor_pdb2 system test]. This is to catch another situation leading to [https://gna.org/bugs/?22505 bug #22505, the failure of the structure.create_diff_tensor_pdb user function when no structural data is present].
* Added an optimisation script for the test_suite/shared_data/diffusion_tensor/ellipsoid relaxation data. This is to help catch [https://gna.org/bugs/?22502 bug #22502, the geometric prolate diffusion representation does not align with axis in PDB], as reported by [https://{{gna link|url=gna.org/users/mab |text=Martin Ballaschk]}}. 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.
* Updated the diffusion tensor PDB representation files. This replaces the broken prolate representation with the corrected representation.
* Deleted the duplicated [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb Structure.test_create_diff_tensor_pdb system test].
* Fix for [https://gna.org/bugs/?22505 bug #22505, the failure of the structure.create_diff_tensor_pdb user function when no structural data is present]. The solution was simple - the CoM of the representation is set to the origin when no structural data is present, and the check for the presence of data removed.
* Another fix for [https://gna.org/bugs/?22505 bug #22505, 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.
* Fix for [https://gna.org/bugs/?22502 bug #22502, the problem whereby the geometric prolate diffusion representation does not align with axis in PDB], as reported by [https://{{gna link|url=gna.org/users/mab |text=Martin Ballaschk]}}. 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.
* Fix for time not extracted for CPMG experiments in target_function. [https://gna.org/bugs/?22461 Bug #22461: NS R1rho 2-site_fit_r1 has extremely high &chi;<sup>2</sup> value in system test Relax_disp.test_r1rho_kjaergaard_missing_r1].
* Fix for interpolating time points, when producing xmgrace files for CPMG experiments. [https://gna.org/bugs/?22461 Bug #22461: NS R1rho 2-site_fit_r1 has extremely high &chi;<sup>2</sup> value in system test Relax_disp.test_r1rho_kjaergaard_missing_r1].
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