Hi Edward. I will remove the nesting of IT99, since it also worried me.
But do you really intent to stay on the argument that nesting should always be from CR72? What if the model pipe for B14 is available. Or from NS CPMG 2-site expanded ? Is this issue rather related how to sort the models first? Best Troels 2014-08-18 16:41 GMT+02:00 Edward d'Auvergne <[email protected]>: > Note that I used the CR72 model as a base for many other slow exchange > models as it is a robust and quick solution which in most cases > accurately approximates the parameters of other models, especially the > numeric models. > > Regards, > > Edward > > > On 18 August 2014 16:38, Edward d'Auvergne <[email protected]> wrote: >> Hi, >> >> The model IT99 is extremely different to all other models, hence it is >> not nested in the auto-analysis. No other model approximates it >> parameters in any meaningful sense. See >> test_suite/shared_data/dispersion/software_comparison for example. I >> think that the model IT99 should have no corresponding nested model: >> >> MODEL_NESTING = { >> ... >> MODEL_IT99: None >> ... >> } >> >> To see this problem, just take any test data and optimise both CR72 >> and IT99 and see if you can get any parameters to be close between the >> two models. The new model nesting protocol is really starting to >> worry me. Why did it change in the first place? >> >> Regards, >> >> Edward >> >> >> >> >> On 12 August 2014 10:54, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Tue Aug 12 10:54:49 2014 >>> New Revision: 24988 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=24988&view=rev >>> Log: >>> Fix for nesting kex, when model is CR72, and analysed models is IT99. >>> >>> sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation >>> rate for the off-resonance R1rho relaxation dispersion models. >>> >>> Modified: >>> branches/R1_fitting/specific_analyses/relax_disp/variables.py >>> >>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>> >>> Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24988&r1=24987&r2=24988&view=diff >>> ============================================================================== >>> --- branches/R1_fitting/specific_analyses/relax_disp/variables.py >>> (original) >>> +++ branches/R1_fitting/specific_analyses/relax_disp/variables.py Tue >>> Aug 12 10:54:49 2014 >>> @@ -911,6 +911,10 @@ >>> elif param == 'phi_ex' and compa_model.model in >>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG and model in >>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG: >>> continue >>> >>> + # Special situation, where 'kex'=1/tex can still be nested >>> from IT99 model. >>> + elif param == 'tex' and compa_model.model in >>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG and model in >>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG: >>> + continue >>> + >>> # Else break out of the loop. >>> else: >>> # Break the for loop, if not found. >>> @@ -953,6 +957,13 @@ >>> if compa_model.model in MODEL_LIST_R1RHO_W_R1_ONLY + >>> MODEL_LIST_R1RHO_FIT_R1_ONLY: >>> return model_info, compa_model >>> >>> + # Special case for IT99. >>> + elif model in [MODEL_IT99]: >>> + # Loop over the models. >>> + for compa_model in compa_models: >>> + # If one of the comparable models is in list with R1rho >>> R1, return this. >>> + if compa_model.model in MODEL_LIST_ANALYTIC_CPMG + >>> MODEL_LIST_NUMERIC_CPMG: >>> + return model_info, compa_model >>> >>> # If there is no comparable models according to EXP_TYPE, check if >>> some models can be nested anyway. >>> else: >>> >>> Modified: >>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py?rev=24988&r1=24987&r2=24988&view=diff >>> ============================================================================== >>> --- >>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>> (original) >>> +++ >>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>> Tue Aug 12 10:54:49 2014 >>> @@ -151,9 +151,27 @@ >>> model = MODEL_CR72 >>> >>> # Test the return. >>> - print nesting_model(self_models=self_models, model=model) >>> self.assertEqual(nesting_model(self_models=self_models, >>> model=model)[1].model, MODEL_LM63) >>> >>> + ## Test MODEL_IT99 model request, when models are CR72. >>> + # Define all the models tested in the analysis. >>> + self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_CR72, MODEL_IT99] >>> + >>> + # Define which current model is selected >>> + model = MODEL_IT99 >>> + >>> + # Test the return. >>> + self.assertEqual(nesting_model(self_models=self_models, >>> model=model)[1].model, MODEL_CR72) >>> + >>> + ## Test MODEL_CR72 model request, when models are MODEL_IT99. >>> + # Define all the models tested in the analysis. >>> + self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_IT99, MODEL_CR72] >>> + >>> + # Define which current model is selected >>> + model = MODEL_CR72 >>> + >>> + # Test the return. >>> + self.assertEqual(nesting_model(self_models=self_models, >>> model=model)[1].model, MODEL_IT99) >>> >>> >>> def test_nesting_model_cpmg_mmq(self): >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-commits mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
