mailr21755 - /trunk/auto_analyses/relax_disp.py


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Posted by edward on December 03, 2013 - 17:36:
Author: bugman
Date: Tue Dec  3 17:36:11 2013
New Revision: 21755

URL: http://svn.gna.org/viewcvs/relax?rev=21755&view=rev
Log:
Added the 'NS MMQ 3-site' models to the dispersion auto-analysis.

This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG dispersion 
models.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.


Modified:
    trunk/auto_analyses/relax_disp.py

Modified: trunk/auto_analyses/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=21755&r1=21754&r2=21755&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp.py (original)
+++ trunk/auto_analyses/relax_disp.py Tue Dec  3 17:36:11 2013
@@ -36,7 +36,7 @@
 from pipe_control.pipes import has_pipe
 from prompt.interpreter import Interpreter
 from specific_analyses.relax_disp.disp_data import has_exponential_exp_type, 
has_cpmg_exp_type, has_fixed_time_exp_type, has_r1rho_exp_type, loop_frq
-from specific_analyses.relax_disp.variables import MODEL_CR72, 
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, 
MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, 
MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, 
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_LIST_NUMERIC, 
MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import MODEL_CR72, 
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, 
MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, 
MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, 
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, 
MODEL_NS_R1RHO_2SITE, MODEL_LIST_NUMERIC, MODEL_R2EFF, MODEL_TAP03, 
MODEL_TP02, MODEL_TSMFK01
 from status import Status; status = Status()
 
 
@@ -236,6 +236,13 @@
             nested_pipe = MODEL_NS_CPMG_2SITE_3D
         if model == MODEL_NS_CPMG_2SITE_STAR_FULL and 
MODEL_NS_CPMG_2SITE_STAR in self.models:
             nested_pipe = MODEL_NS_CPMG_2SITE_STAR
+        if model == MODEL_NS_MMQ_3SITE_LINEAR and MODEL_MMQ_2SITE in 
self.models:
+            nested_pipe = MODEL_MMQ_2SITE
+        if model == MODEL_NS_MMQ_3SITE:
+            if MODEL_NS_MMQ_3SITE_LINEAR in self.models:
+                nested_pipe = MODEL_NS_MMQ_3SITE_LINEAR
+            elif MODEL_MMQ_2SITE in self.models:
+                nested_pipe = MODEL_MMQ_2SITE
 
         # Using the analytic solution.
         analytic = False
@@ -476,7 +483,7 @@
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='i0', file='i0.agr', dir=path, force=True)
 
         ## The R20 parameter.
-        #if has_cpmg_exp_type() and model in [None, MODEL_LM63, MODEL_CR72, 
MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_MQ_CR72, 
MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_EXPANDED]:
+        #if has_cpmg_exp_type() and model in [None, MODEL_LM63, MODEL_CR72, 
MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_MQ_CR72, 
MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
         #    self.interpreter.value.write(param='r2', file='r20.out', 
dir=path, force=True)
         #    self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='r2', file='r20.agr', dir=path, force=True)
 
@@ -492,12 +499,15 @@
         #    self.interpreter.value.write(param='r2', file='r1rho0.out', 
dir=path, force=True)
         #    self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='r2', file='r1rho0.agr', dir=path, force=True)
 
-        # The pA and pB parameters.
-        if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, 
MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, 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, MODEL_TAP03, MODEL_MP05]:
+        # The pA, pB, and pC parameters.
+        if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, 
MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, 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, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
             self.interpreter.value.write(param='pA', file='pA.out', 
dir=path, force=True)
             self.interpreter.value.write(param='pB', file='pB.out', 
dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='pA', file='pA.agr', dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='pB', file='pB.agr', dir=path, force=True)
+        if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
+            self.interpreter.value.write(param='pC', file='pC.out', 
dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='pC', file='pC.agr', dir=path, force=True)
 
         # The Phi_ex parameter.
         if model in [None, MODEL_LM63, MODEL_M61, MODEL_DPL94]:
@@ -515,11 +525,25 @@
         if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, 
MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, 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, MODEL_TAP03, MODEL_MP05, MODEL_TSMFK01]:
             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)
+        if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
+            self.interpreter.value.write(param='dw_AB', file='dw_AB.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='dw_BC', file='dw_BC.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='dw_AC', file='dw_AC.out', 
dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dw_AB', file='dw_AB.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dw_BC', file='dw_BC.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dw_AC', file='dw_AC.agr', dir=path, force=True)
 
         # The dwH parameter.
         if model in [None, MODEL_MQ_CR72, MODEL_MMQ_2SITE]:
             self.interpreter.value.write(param='dwH', file='dwH.out', 
dir=path, force=True)
             self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dwH', file='dwH.agr', dir=path, force=True)
+        if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
+            self.interpreter.value.write(param='dwH_AB', file='dwH_AB.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='dwH_BC', file='dwH_BC.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='dwH_AC', file='dwH_AC.out', 
dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dwH_AB', file='dwH_AB.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dwH_BC', file='dwH_BC.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dwH_AC', file='dwH_AC.agr', dir=path, force=True)
 
         # 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_MQ_CR72, 
MODEL_MMQ_2SITE, 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, MODEL_TAP03, 
MODEL_MP05]:
@@ -529,6 +553,13 @@
             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)
+        if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
+            self.interpreter.value.write(param='kex_AB', file='kex_AB.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='kex_BC', file='kex_BC.out', 
dir=path, force=True)
+            self.interpreter.value.write(param='kex_AC', file='kex_AC.out', 
dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex_AB', file='kex_AB.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex_BC', file='kex_BC.agr', dir=path, force=True)
+            self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex_AC', file='kex_AC.agr', dir=path, force=True)
 
         # The k_AB parameter.
         if model in [None, MODEL_TSMFK01]:

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