r20966 - in /branches/relax_disp: auto_analyses/ specific_analyses/relax_disp/ test_suite/system_tests/ -- September 10, 2013 - 14:39

Author: bugman
Date: Tue Sep 10 14:39:51 2013
New Revision: 20966

URL: http://svn.gna.org/viewcvs/relax?rev=20966&view=rev
Log:
Added the conversion to k_AB from kex and pA. k_AB = kex * (1.0 - pA).

Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of 
Tollinger/Kay dispersion model (2001)
Following the guide at: 
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ 
gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@xxxxxxxxxxxxx>

Modified:
    branches/relax_disp/auto_analyses/relax_disp.py
    branches/relax_disp/specific_analyses/relax_disp/api.py
    branches/relax_disp/specific_analyses/relax_disp/parameters.py
    branches/relax_disp/test_suite/system_tests/relax_disp.py

Modified: branches/relax_disp/auto_analyses/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=20966&r1=20965&r2=20966&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Tue Sep 10 14:39:51 2013
@@ -417,10 +417,12 @@
             self.interpreter.value.write(param='dw', file='dw.out', 
dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dw', file='dw.agr', dir=path, force=True)
 
-        # The kex and tex parameters.
+        # The k_AB, kex and tex parameters.
         if model in [None, MODEL_LM63, MODEL_CR72, MODEL_CR72_FULL, 
MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_NS_CPMG_2SITE_3D, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, 
MODEL_NS_R1RHO_2SITE, MODEL_TP02]:
+            self.interpreter.value.write(param='k_AB', file='k_AB.out', 
dir=path, force=True)
             self.interpreter.value.write(param='kex', file='kex.out', 
dir=path, force=True)
             self.interpreter.value.write(param='tex', file='tex.out', 
dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='k_AB', file='k_AB.agr', dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex', file='kex.agr', dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='tex', file='tex.agr', dir=path, force=True)
 

Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20966&r1=20965&r2=20966&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Sep 10 
14:39:51 2013
@@ -1517,6 +1517,9 @@
         pairs['pA'] = 'pB'
         pairs['pB'] = 'pA'
 
+        # Add the names of kex-k_AB pair.
+        pairs['k_AB'] = 'kex'
+
         # Get the minimisation statistic object names.
         min_names = self.data_names(set='min')
 

Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20966&r1=20965&r2=20966&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Tue Sep 10 
14:39:51 2013
@@ -716,6 +716,13 @@
             tex = 1.0 / (2.0 * value)
             set_value(value=tex, key=key, spins=spins, sim_index=sim_index, 
param_name='tex', spin_index=spin_index, frq_index=frq_index)
 
+        # The kex to k_AB conversion.
+        if param_name == 'kex':
+            # Get pA value.
+            pA = get_value(key=key, spins=spins, sim_index=sim_index, 
param_name='pA', spin_index=spin_index, frq_index=frq_index)
+            k_AB = value * (1.0 - pA)
+            set_value(value=k_AB, key=key, spins=spins, sim_index=sim_index, 
param_name='k_AB', spin_index=spin_index, frq_index=frq_index)
+
         # The tex to kex conversion.
         if param_name == 'tex':
             kex = 1.0 / (2.0 * value)

Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=20966&r1=20965&r2=20966&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Sep 10 
14:39:51 2013
@@ -1014,6 +1014,9 @@
         self.assertAlmostEqual(res61L.kex, 609.262167216419, 0)
         self.assertAlmostEqual(res61L.chi2, 65.99987828889657, 5)
 
+        # Test the conversion to k_AB from kex and pA.
+        self.assertEqual(res61L.k_AB, res61L.kex * (1.0 - res61L.pA))
+
 
     def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72_full(self):
         """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.