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Relax 3.3.0

1,033 bytes added, 18:00, 23 September 2014
→‎Changes: More API links.
* Code validation of [http://www.nmr-relax.com/api/3.3/lib.dispersion.tp02-module.html lib/dispersion/tp02.py]. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Code validation of [http://www.nmr-relax.com/api/3.3/lib.dispersion.two_point-module.html lib/dispersion/two_point.py]. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Code validation of [http://www.nmr-relax.com/api/3.3/target_functions.relax_disp-module.html target_functions/relax_disp.py]. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* For model [[NS MMQ 3-site]], moved the parameter conversion of &Delta;&omega;<sub>AB</sub> from target function to lib function. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Removed chi sum initialisation in func_ns_mmq_2site() as this is not used. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Documentation fix for the [http://www.nmr-relax.com/api/3.3/target_functions.relax_disp.Dispersion-class.html#get_back_calc get_back_calc() function in target_function/relax_disp.py]. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Removed unnecessary repetitive calculation of k<sub>ex</sub><sup>2</sup> in model [[DPL94]]. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* API documentation fixes, where a "\" is the last character on the line. There should be a space " ", ending this character. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Renamed function to represent the functionality of returning data in correct xmgrace form. Also improved the epydoc information, for the return of values. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].
* Renamed the other function to represent the functionality of returning data in correct xmgrace form. Also improved the epydoc information, for the return of values. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].
* Added function to calculate rotating frame parameters for [http://www.nmr-relax.com/api/3.3/lib.nmr-module.html lib/nmr.py]. This function is called several times in [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.data-module.html specific_analyses/relax_disp/data.py ] by plotting functions. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].* Replaced repeated calculation of rotating frame parameters to use function in [http://www.nmr-relax.com/api/3.3/lib.nmr-module.html lib/nmr.py]. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].
* Skip production of plotting R<sub>1&rho;</sub>/R<sub>2</sub> as function of effective field &omega;<sub>eff</sub>, when spin.isotope is not present. This can happen when it is 'exp_fit' model curve fitting. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].
* Added functionality to function to accept how the first part of the filename is formed. This is to prepare to reuse the same plotting function. [https://gna.org/support/?3124 Sr #3124: Grace graphs production for R<sub>1&rho;</sub> analysis with R<sub>2eff</sub> as function of &Omega;<sub>eff</sub>]. [https://gna.org/support/?3138 Sr #3138: Interpolating &theta; through spin-lock offset &Omega;, rather than spin-lock field strength &omega;<sub>1</sub>].
* Added a "check" function, what will determine if R<sub>1</sub> data is missing for a model to analyse. Also added corresponding unit tests, to test the functionality.
* Modified in documentation, that the [[No Rex]] model have one chemical exchange site, namely itself.
* Copied [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.variables-module.html variables.py ] to [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.model-module.html model.py]. There should not exist any functions in [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.variables-module.html variables.py]. It should only consist of hardcoded variables, and the functions related to model sorting and nesting is split into its own file.* Parted the file of [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.variables-module.html variables.py ] into [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.model-module.html model.py].* Removed the unit test regarding [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.model-module.html model.py ] in test_variables.py.* Added unit tests regarding [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.model-module.html model.py and its functions].
* Removed the auto-sorting of models, when performing auto analysis of Relaxation dispersion. This was discussed in: http://thread.gmane.org/gmane.science.nmr.relax.scm/22733, http://thread.gmane.org/gmane.science.nmr.relax.scm/22734, http://thread.gmane.org/gmane.science.nmr.relax.scm/22737. Through this discussion, it has appeared that the order of how models are sorted for analysis, and hence the possibility for nesting, is a complicated case. The order of analysis should be possible to manually put into the auto analysis. This was not the scope of [https://gna.org/support/?3135 sr #3135: Optimisation of the R<sub>1</sub> relaxation rate for the off-resonance R<sub>1&rho;</sub> relaxation dispersion models] to implement such a feature. Such a feature could be implemented for the next version of relax. It could be designed as function to "suggest" an order in the GUI. But this functionality would have to wait.
* Removing the t<sub>ex</sub>->k<sub>ex</sub> conversion, and &phi;<sub>ex</sub> from &Delta;&omega; and p<sub>A</sub>. This solution is not a proper implementation, but these parameters should rather be found by grid search.
* Added definition and dictionary, for each model, to determine which model they nest from. This is better to hardcode, since it makes it possible to produce a table with an overview, and accurately determine which model is nested from. This is discussed in thread http://thread.gmane.org/gmane.science.nmr.relax.devel/6684.
* Moved the lookup in dictionaries for model information, into the class of model info.
* Division of unit tests of [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.model-module.html specific_analyses/relax_disp/model.py ] into different functions. Also added more print information to each tests.
* Added the ordered list of nest models to the class of model information.
* Modified the defined list of nesting, according to thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/6684. More specific, thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/6694.
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