Changes

Jump to navigation Jump to search

Tutorial for adding relaxation dispersion models to relax

98 bytes added, 17:18, 18 November 2015
β†’β€ŽThe test suite: Improved formatting using the <code> tag.
This step is normally performed first. This is the most important part that makes sure that the code not only works now, but will continue working for the entire lifetime of the relax project.
The idea is that real or synthetic data, for example as Sparky peak lists, is obtained or created for the model and added to the test suite directory <code>test_suite/shared_data/dispersion/</code>. This is then used in a system test to check that the code in relax can consistently reproduce the results.
=== Synthetic data ===
=== Measured data ===
An alternative is to use real measured relaxation dispersion data. This data should be added as peak lists containing peak intensities to <code>test_suite/shared_data/dispersion/</code>. As the real solution cannot be known a priori, the results from relax must be compared to results obtained from another software program (possibly directly from a publication). The steps required for using such data are:
* Create a new directory name for the test data.
* Add the original full peak lists to the directory.
* Make truncated versions of these files (ending in <code>_trunc.*</code>) and add these as well. These will be used for the system test instead of the full data to allow the test to finish in a reasonable amount of time.
* Add a script which performs the full analysis in relax for the model. Also a script which performs the analysis using only the [[R2eff ]] model. See the '''<code>test_suite/shared_data/dispersion/Hansen/*.py''' </code> scripts for reference - these scripts should be copied to your data directory and modified (using the '''<code>svn cp''' </code> command). Once the scripts are functional, they can be copied and modified for the truncated data (again using the '''<code>svn cp''' </code> command).
* Copy the full analysis script to '''<code>test_suite/system_tests/scripts/relax_disp/''' </code> with an appropriate name (always using the '''<code>svn cp''' </code> command). This can then be used in a new system test. Better still, the final save file from the '''<code>r2eff_calc.py''' </code> script for the truncated data can be used to start the script. This is again to save a lot of computation time in the test. See the '''<code>test_tp02_data_to_ns_r1rho_2site()''' </code> system test in the '''<code>test_suite/system_tests/relax_disp.py''' </code> file for a template.
If you are not a relax developer, a [https://gna.org/projects/relax support request] can be [https://gna.org/support/?func=additem&group=relax submitted]. You can attach files and add comments to that request for a relax developer to make the changes for you.
* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18256 r20500] [http://article.gmane.org/gmane.science.nmr.relax.scm/18293 r20538] [http://article.gmane.org/gmane.science.nmr.relax.scm/18295 r20541] [http://article.gmane.org/gmane.science.nmr.relax.scm/18297 r20537]
* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17647 r19891] [http://article.gmane.org/gmane.science.nmr.relax.scm/17648 r19892] [http://article.gmane.org/gmane.science.nmr.relax.scm/17649 r19893] [http://article.gmane.org/gmane.science.nmr.relax.scm/17662 r19906] [http://article.gmane.org/gmane.science.nmr.relax.scm/17663 r19907]
 
== Creating a new experiment type ==
Trusted, Bureaucrats
4,223

edits

Navigation menu