Difference between revisions of "Relax 3.1.7"
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== Changes == | == Changes == | ||
| − | * Added text file for the articles reference values from the global fit in Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is from optimisation of the Kjaergaard et al., 2013 Off-resonance | + | * Added text file for the articles reference values from the global fit in Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is from optimisation of the Kjaergaard et al., 2013 Off-resonance R<sub>1ρ</sub> relaxation dispersion experiments using the 'DPL' model. This uses the data from Kjaergaard's paper at DOI: http://dx.doi.org/10.1021/bi4001062. |
* Replaced "_" with "-" in text file with global fit residues. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Replaced "_" with "-" in text file with global fit residues. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
* Sorted the reference values in residue order. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Sorted the reference values in residue order. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
| − | * Added reference data and guess data for a global fit | + | * Added reference data and guess data for a global fit R<sub>1ρ</sub> analysis. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This system test is setup comparison with paper values, and will be turned off later to prevent long running time. |
* Redid dict() keys for unit test of find_intensity_keys(), to pass on Python 3.2 and 3.3. Work in progress for [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is a response to message: http://thread.gmane.org/gmane.science.nmr.relax.devel/5132. | * Redid dict() keys for unit test of find_intensity_keys(), to pass on Python 3.2 and 3.3. Work in progress for [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is a response to message: http://thread.gmane.org/gmane.science.nmr.relax.devel/5132. | ||
* Added ":" to dictionary keys to match return from spin_loop in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Added ":" to dictionary keys to match return from spin_loop in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
| − | * Removed model | + | * Removed model [[No Rex]] to be tested in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. |
* Aliased spins in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Aliased spins in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
| − | * Set opt_func_tol = 1e-15 and opt_max_iterations = 100000 to run system test Relax_disp.test_r1rho_kjaergaard faster. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | + | * Set opt_func_tol = 1e<sup>-15</sup> and opt_max_iterations = 100000 to run system test Relax_disp.test_r1rho_kjaergaard faster. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. |
* Re-ordered code lines in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Re-ordered code lines in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
* Assigned guess values for system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Assigned guess values for system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
* Added a section at the start of the dispersion GUI analysis tutorial about 'computation time'. This is for the dispersion chapter of the manual. | * Added a section at the start of the dispersion GUI analysis tutorial about 'computation time'. This is for the dispersion chapter of the manual. | ||
* Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard. Work in progress for [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | * Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard. Work in progress for [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. | ||
| − | * Added fitted R1 values from paper to system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added fitted R1 values from paper to system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This will be used to test the output of calculating Ω<sub>eff</sub>, as stated in http://article.gmane.org/gmane.science.nmr.relax.devel/5148. |
| − | * Added reading of R1 values in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added reading of R1 values in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added full manual steps of analysis for system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added full manual steps of analysis for system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Modified the directory separator from "/" to os.sep in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Modified the directory separator from "/" to os.sep in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Commented out the commands for writing of text files and state files to speed up system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Commented out the commands for writing of text files and state files to speed up system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added the testing of writing out theta values in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added the testing of writing out θ values in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added the parameter "theta" to specific_analyses/relax_disp/api.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added the parameter "theta" to specific_analyses/relax_disp/api.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Modified parameter py_type to dict() for the theta value. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Modified parameter py_type to dict() for the θ value. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added parameter "theta" do description tables. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added parameter "theta" do description tables. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Made an assertion that spin contains attribute "theta" in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Made an assertion that spin contains attribute "theta" in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added unit test for return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added unit test for return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is development according to thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5157. |
| − | * Commented out the expectation of the attribute "theta" to exist in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Commented out the expectation of the attribute "theta" to exist in system test Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Imported return_param_key_from_data to be used in unit test return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Imported return_param_key_from_data to be used in unit test return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
* The relax information printout, from "relax -i" for example, now includes detailed CPU information. This uses operating system specific commands to obtain this information which is not available from the platform Python module. | * The relax information printout, from "relax -i" for example, now includes detailed CPU information. This uses operating system specific commands to obtain this information which is not available from the platform Python module. | ||
* Removed the dependence on subprocess.check_output() as this is only for Python 2.7 and higher. This is for the relax information printout about the CPU info recently introduced. | * Removed the dependence on subprocess.check_output() as this is only for Python 2.7 and higher. This is for the relax information printout about the CPU info recently introduced. | ||
* The RAM in the relax information printout is now displayed for Mac OS X. The 'sysctl' command is now being used to retrieve the RAM size and total memory, and the swap is calculated as the difference. | * The RAM in the relax information printout is now displayed for Mac OS X. The 'sysctl' command is now being used to retrieve the RAM size and total memory, and the swap is calculated as the difference. | ||
* Added the OMP relaxation rates and compressed PDB file to the repository. This is to allow users to have a full data set to perform a test model-free analysis with. | * Added the OMP relaxation rates and compressed PDB file to the repository. This is to allow users to have a full data set to perform a test model-free analysis with. | ||
| − | * Added a sample_script to generate theta values for | + | * Added a sample_script to generate θ values for R<sub>1ρ</sub> data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. The script is explained at the wiki: http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data. |
* Created a new citation for relax which concatenates both the d'Auvergne and Gooley 2008 papers. This is to show to those who are unaware of back-to-back paper concatenation rules how to cite both papers using one reference, saving a lot of space. | * Created a new citation for relax which concatenates both the d'Auvergne and Gooley 2008 papers. This is to show to those who are unaware of back-to-back paper concatenation rules how to cite both papers using one reference, saving a lot of space. | ||
| − | * Added lib.rotating_frame module containing functions related to rotating frame NMR calculations. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added lib.rotating_frame module containing functions related to rotating frame NMR calculations. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added rotating_frame to lib.__init__.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added rotating_frame to lib.__init__.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added unit test file _lib.test_rotating_frame.py to __init__.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added unit test file _lib.test_rotating_frame.py to __init__.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added unit test file _lib.test_rotating_frame(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added unit test file _lib.test_rotating_frame(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. These unit test will be used to calculate and return dictionaries of tilt_angles, Delta_omega and omega_eff. Some of the R<sub>1ρ</sub> data mentioned in: http://www.nmr-relax.com/manual/Dispersion_model_summary.html. |
| − | * Added link to manual for calculating NMR parameters in the doctring for lib.rotating_frame.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added link to manual for calculating NMR parameters in the doctring for lib.rotating_frame.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Renamed function "calc_tilt_angle" to "calc_rotating_frame_params" in lib.rotating_frame. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Renamed function "calc_tilt_angle" to "calc_rotating_frame_params" in lib.rotating_frame. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is to reflect, that the function should return and store spin values of both tilt_angles, Delta_omega and omega_eff. |
| − | * Replaced with calc_rotating_frame_params in unit test, to reflect function renaming. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Replaced with calc_rotating_frame_params in unit test, to reflect function renaming. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Improved docstring in lib.rotating_frame. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Improved docstring in lib.rotating_frame. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
* Rearranged the citations in the citations chapter. The references for relax are now far more prominent. | * Rearranged the citations in the citations chapter. The references for relax are now far more prominent. | ||
| − | * Implemented the return of Delta_omega = "average resonance offset in the rotating frame" in specific_analysis.relax_disp.return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Implemented the return of Delta_omega = "average resonance offset in the rotating frame" in specific_analysis.relax_disp.return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fixed unpacking of return from function calls of return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fixed unpacking of return from function calls of return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the effective field in rotating frame in rad/s. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the effective field in rotating frame in rad/s. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fixed unpacking of return from function calls of return_offset_data, since | + | * Fixed unpacking of return from function calls of return_offset_data, since &omega<sub>eff</sub> is now also returned. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Moved calc_rotating_frame_params() to specific_analysis.relax_disp.disp_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Moved calc_rotating_frame_params() to specific_analysis.relax_disp.disp_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is in a response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html. |
| − | * Started unit test for _specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Started unit test for _specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is in response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html. |
| − | * Removed lib.test_rotating_frame.py and the associated unit test. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Removed lib.test_rotating_frame.py and the associated unit test. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is in response to http://www.mail-archive.com/relax-devel@gna.org/msg05080.html. |
| − | * Made calc_rotating_frame_params take spin "The spin system specific data container" as input. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Made calc_rotating_frame_params take spin "The spin system specific data container" as input. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Modified calc_rotating_frame_params() to operate on the level of spin container and ID. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Modified calc_rotating_frame_params() to operate on the level of spin container and ID. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Modified unit test test_calc_rotating_frame_params to use spin container and ID in test. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Modified unit test test_calc_rotating_frame_params to use spin container and ID in test. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
* Epydoc docstring fix for the Structure.test_bug_21522_master_record_atom_count system test. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html. | * Epydoc docstring fix for the Structure.test_bug_21522_master_record_atom_count system test. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html. | ||
* Epydoc docstring fix for the SetValue() method of the File input GUI element. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html. | * Epydoc docstring fix for the SetValue() method of the File input GUI element. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html. | ||
* Removed the test_suite/shared_data directory from the API documentation scanning. This is to avoid trying to import the frame order relax scripts which cannot be imported into Python. | * Removed the test_suite/shared_data directory from the API documentation scanning. This is to avoid trying to import the frame order relax scripts which cannot be imported into Python. | ||
| − | * Added epydoc information about dimensions for w_e in function return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added epydoc information about dimensions for w_e in function return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added verbosity flag to calc_rotating_frame_params() to allow switching of print information. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added verbosity flag to calc_rotating_frame_params() to allow switching of print information. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added unit test for use of value.write to write theta values calculated from calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added unit test for use of value.write to write θ values calculated from calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Extended unit test for use of value.write to write intensities file. This is to test that changing of the API function will retain its function. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Extended unit test for use of value.write to write intensities file. This is to test that changing of the API function will retain its function. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Replaced API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta when this is requested. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Replaced API function in specific_analysis.relax_disp.api to calculate and return values for parameter θ when this is requested. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html. |
| − | * Extended API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta when this is requested. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Extended API function in specific_analysis.relax_disp.api to calculate and return values for parameter θ when this is requested. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html. |
| − | * Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Extended unit test test_value_write_calc_rotating_frame_params() to also test writing of | + | * Extended unit test test_value_write_calc_rotating_frame_params() to also test writing of &omega<sub>eff</sub> values. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fixed typo and removed grace string for parameter description of theta. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fixed typo and removed grace string for parameter description of θ. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added handling of calculating | + | * Added handling of calculating &omega<sub>eff</sub> in dispersion API. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added unit to parameter description of theta and | + | * Added unit to parameter description of θ and &omega<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fix for field count and added check for | + | * Fix for field count and added check for R<sub>1ρ</sub> type in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added grace string to parameter description of theta and | + | * Added grace string to parameter description of θ and &omega<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fixed code duplication in relax_disp API, for calculation of theta and | + | * Fixed code duplication in relax_disp API, for calculation of θ and &omega<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Removed unused lines of code in unit test test_return_offset_data(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Removed unused lines of code in unit test test_return_offset_data(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Moved unit test of value writing of calc_rotating_frame_params() into separate system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Moved unit test of value writing of calc_rotating_frame_params() into separate system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is to test the auto_analysis value.write function to write θ and &omega<sub>eff</sub> values for an R<sub>1ρ</sub> setup. |
| − | * Added writing of parameters theta and | + | * Added writing of parameters θ and &omega<sub>eff</sub> for an auto-analysis if model in MODEL_LIST_R1RHO_FULL. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added return of None values for function calc_rotating_frame_params() if spin is not selected. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added return of None values for function calc_rotating_frame_params() if spin is not selected. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Extended system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of theta values. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Extended system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of θ values. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Hardcoded the writing of | + | * Hardcoded the writing of R<sub>2eff</sub> as function of the tilt angle θ, when using the user function relax_disp.write_disp_curves. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. θ values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL. |
| − | * Fix for return of None tuble in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fix for return of None tuble in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Hardcoded contents of writing of parameters theta and | + | * Hardcoded contents of writing of parameters θ and &omega<sub>eff</sub> in system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is to better support testing of key ordering and different architectures, etc. |
| − | * Fixed code duplication in specific_analysis.relax_disp.disp_data.write_disp_curves(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fixed code duplication in specific_analysis.relax_disp.disp_data.write_disp_curves(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Modified system test of hardcoded values of theta and | + | * Modified system test of hardcoded values of θ and &omega<sub>eff</sub> to match precision to 14 digits. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of | + | * Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of R<sub>1ρ</sub> type. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This was discovered using the system tests. |
| − | * Fix for calculating the theta angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Fix for calculating the θ angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This follows discussion in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205. |
| − | * Modified unit and system test to reflect new calculation of rotating frame tilt angle | + | * Modified unit and system test to reflect new calculation of rotating frame tilt angle θ. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This was discussed in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205. |
| − | * Added interpolation calculation of theta and | + | * Added interpolation calculation of θ and &omega<sub>eff</sub>, when dispersion points are interpolated. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
| − | * Added printout of Omega, the average resonance offset, in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for | + | * Added printout of Ω, the average resonance offset, in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. |
Revision as of 17:10, 9 September 2014
Contents
Description
This is a minor feature and bugfix release which includes improvements to the relaxation dispersion chapter of the manual and the addition of new infrastructure for R1ρ data handling in the dispersion analysis. More details are given below.
Download
The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).
CHANGES file
Version 3.1.7 (17 March 2014, from /trunk) http://svn.gna.org/svn/relax/tags/3.1.7
Features
- Large amounts of new infrastructure for the R1ρ relaxation dispersion analysis type.
- More hardware information printed out when using the '--info' command line option.
- The user function relax_disp.write_disp_curves now produces text files of R2eff verses the rotating frame tilt angle θ.
- Small improvements for the relaxation dispersion GUI tutorial and citation chapter of the relax manual.
Changes
- Added text file for the articles reference values from the global fit in Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths. This is from optimisation of the Kjaergaard et al., 2013 Off-resonance R1ρ relaxation dispersion experiments using the 'DPL' model. This uses the data from Kjaergaard's paper at DOI: http://dx.doi.org/10.1021/bi4001062.
- Replaced "_" with "-" in text file with global fit residues. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Sorted the reference values in residue order. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Added reference data and guess data for a global fit R1ρ analysis. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths. This system test is setup comparison with paper values, and will be turned off later to prevent long running time.
- Redid dict() keys for unit test of find_intensity_keys(), to pass on Python 3.2 and 3.3. Work in progress for bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths. This is a response to message: http://thread.gmane.org/gmane.science.nmr.relax.devel/5132.
- Added ":" to dictionary keys to match return from spin_loop in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Removed model No Rex to be tested in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Aliased spins in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Set opt_func_tol = 1e-15 and opt_max_iterations = 100000 to run system test Relax_disp.test_r1rho_kjaergaard faster. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Re-ordered code lines in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Assigned guess values for system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Added a section at the start of the dispersion GUI analysis tutorial about 'computation time'. This is for the dispersion chapter of the manual.
- Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard. Work in progress for bug #21344, handling of in sparse acquired R1ρ dataset with missing combinations of time and spin-lock field strengths.
- Added fitted R1 values from paper to system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This will be used to test the output of calculating Ωeff, as stated in http://article.gmane.org/gmane.science.nmr.relax.devel/5148.
- Added reading of R1 values in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added full manual steps of analysis for system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Modified the directory separator from "/" to os.sep in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Commented out the commands for writing of text files and state files to speed up system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added the testing of writing out θ values in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added the parameter "theta" to specific_analyses/relax_disp/api.py. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Modified parameter py_type to dict() for the θ value. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added parameter "theta" do description tables. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Made an assertion that spin contains attribute "theta" in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added unit test for return_offset_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is development according to thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5157.
- Commented out the expectation of the attribute "theta" to exist in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Imported return_param_key_from_data to be used in unit test return_offset_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- The relax information printout, from "relax -i" for example, now includes detailed CPU information. This uses operating system specific commands to obtain this information which is not available from the platform Python module.
- Removed the dependence on subprocess.check_output() as this is only for Python 2.7 and higher. This is for the relax information printout about the CPU info recently introduced.
- The RAM in the relax information printout is now displayed for Mac OS X. The 'sysctl' command is now being used to retrieve the RAM size and total memory, and the swap is calculated as the difference.
- Added the OMP relaxation rates and compressed PDB file to the repository. This is to allow users to have a full data set to perform a test model-free analysis with.
- Added a sample_script to generate θ values for R1ρ data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. The script is explained at the wiki: http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data.
- Created a new citation for relax which concatenates both the d'Auvergne and Gooley 2008 papers. This is to show to those who are unaware of back-to-back paper concatenation rules how to cite both papers using one reference, saving a lot of space.
- Added lib.rotating_frame module containing functions related to rotating frame NMR calculations. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added rotating_frame to lib.__init__.py. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added unit test file _lib.test_rotating_frame.py to __init__.py. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added unit test file _lib.test_rotating_frame(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. These unit test will be used to calculate and return dictionaries of tilt_angles, Delta_omega and omega_eff. Some of the R1ρ data mentioned in: http://www.nmr-relax.com/manual/Dispersion_model_summary.html.
- Added link to manual for calculating NMR parameters in the doctring for lib.rotating_frame.py. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Renamed function "calc_tilt_angle" to "calc_rotating_frame_params" in lib.rotating_frame. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is to reflect, that the function should return and store spin values of both tilt_angles, Delta_omega and omega_eff.
- Replaced with calc_rotating_frame_params in unit test, to reflect function renaming. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Improved docstring in lib.rotating_frame. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Rearranged the citations in the citations chapter. The references for relax are now far more prominent.
- Implemented the return of Delta_omega = "average resonance offset in the rotating frame" in specific_analysis.relax_disp.return_offset_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fixed unpacking of return from function calls of return_offset_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the effective field in rotating frame in rad/s. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fixed unpacking of return from function calls of return_offset_data, since &omegaeff is now also returned. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Moved calc_rotating_frame_params() to specific_analysis.relax_disp.disp_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is in a response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.
- Started unit test for _specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is in response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.
- Removed lib.test_rotating_frame.py and the associated unit test. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is in response to http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.
- Made calc_rotating_frame_params take spin "The spin system specific data container" as input. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Modified calc_rotating_frame_params() to operate on the level of spin container and ID. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Modified unit test test_calc_rotating_frame_params to use spin container and ID in test. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Epydoc docstring fix for the Structure.test_bug_21522_master_record_atom_count system test. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html.
- Epydoc docstring fix for the SetValue() method of the File input GUI element. This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html.
- Removed the test_suite/shared_data directory from the API documentation scanning. This is to avoid trying to import the frame order relax scripts which cannot be imported into Python.
- Added epydoc information about dimensions for w_e in function return_offset_data. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added verbosity flag to calc_rotating_frame_params() to allow switching of print information. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added unit test for use of value.write to write θ values calculated from calc_rotating_frame_params(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Extended unit test for use of value.write to write intensities file. This is to test that changing of the API function will retain its function. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Replaced API function in specific_analysis.relax_disp.api to calculate and return values for parameter θ when this is requested. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.
- Extended API function in specific_analysis.relax_disp.api to calculate and return values for parameter θ when this is requested. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.
- Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Extended unit test test_value_write_calc_rotating_frame_params() to also test writing of &omegaeff values. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fixed typo and removed grace string for parameter description of θ. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added handling of calculating &omegaeff in dispersion API. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added unit to parameter description of θ and &omegaeff. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fix for field count and added check for R1ρ type in calc_rotating_frame_params(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added grace string to parameter description of θ and &omegaeff. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fixed code duplication in relax_disp API, for calculation of θ and &omegaeff. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Removed unused lines of code in unit test test_return_offset_data(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Moved unit test of value writing of calc_rotating_frame_params() into separate system tests. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is to test the auto_analysis value.write function to write θ and &omegaeff values for an R1ρ setup.
- Added writing of parameters θ and &omegaeff for an auto-analysis if model in MODEL_LIST_R1RHO_FULL. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added return of None values for function calc_rotating_frame_params() if spin is not selected. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Extended system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of θ values. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Hardcoded the writing of R2eff as function of the tilt angle θ, when using the user function relax_disp.write_disp_curves. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. θ values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.
- Fix for return of None tuble in calc_rotating_frame_params(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Hardcoded contents of writing of parameters θ and &omegaeff in system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This is to better support testing of key ordering and different architectures, etc.
- Fixed code duplication in specific_analysis.relax_disp.disp_data.write_disp_curves(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Modified system test of hardcoded values of θ and &omegaeff to match precision to 14 digits. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of R1ρ type. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This was discovered using the system tests.
- Fix for calculating the θ angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This follows discussion in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
- Modified unit and system test to reflect new calculation of rotating frame tilt angle θ. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff. This was discussed in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
- Added interpolation calculation of θ and &omegaeff, when dispersion points are interpolated. Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
- Added printout of Ω, the average resonance offset, in calc_rotating_frame_params(). Regarding sr #3124, Grace graphs production for R1ρ analysis with R2eff as function of Ωeff.
Bugfixes
- Typo fix for text in the model-free GUI auto-analysis. The maximum iterations for the protocol was misspelled in the GUI. This was spotted by Hessam Nasrollah.
- Fix for one of the frame order system tests when using the Mac OS X application binary. The problem was that the 'shared_data' directory could not be found as it was not included in the test_suite package __all__ list.
- Fix for bug #21754, the failure of the grace.view user function on MS Windows in opening a file in qtgrace when the path includes spaces, as reported by Mengjun Xue (mengjun dott xue att mailbox dott tu-berlin dott de). The fix was to run the program with the file name in double quotes.
- Fix for bug #21763, the problem of the chi2 value not being visible in the parameter list of the grace.write and value.write user functions in the GUI. The problem was that when asking for the parameter name list, the minimisation parameters were not being asked for.
Links
For reference, the following links are also part of the announcement for this release:
