Re: r24988 - in /branches/R1_fitting: specific_analyses/relax_disp/ test_suite/unit_tests/_specific_analyses/_relax_disp/ -- August 18, 2014

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 <edward@xxxxxxxxxxxxx> 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,  <tlinnet@xxxxxxxxxxxxx> 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):


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Re: r24988 - in /branches/R1_fitting: specific_analyses/relax_disp/ test_suite/unit_tests/_specific_analyses/_relax_disp/

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