Merge pull request #339 from upibhalla/master

Fix to CaConc to factor in valence of 2. Update to rdesigneur to hand…

Author: dilawar

biophysics/CaConcBase.cpp

@@ -12,6 +12,8 @@
 #include "../basecode/ElementValueFinfo.h"
 #include "CaConcBase.h"
 
+#define VALENCE 2
+
 ///////////////////////////////////////////////////////
 // MsgSrc definitions
 ///////////////////////////////////////////////////////
@@ -76,7 +78,7 @@ const Cinfo* CaConcBase::initCinfo()
 						    "Volume scaling factor. "
 						    "Deprecated. This is a legacy field from GENESIS and exposes "
 						    "internal calculations. Please do not use. \n"
-						    "B = 1/(vol * F) so that it obeys:\n"
+						    "B = 1/(vol * F* VALENCE) so that it obeys:\n"
 						    "dC/dt = B*I_Ca - C/tau",
 						    &CaConcBase::setB,
 						    &CaConcBase::getB
@@ -260,7 +262,7 @@ void CaConcBase::updateDimensions( const Eref& e )
     double coreRadius = diameter_ / 2.0 - thickness_;
     vol -= PI * coreRadius * coreRadius * length_;
   }
-  double B = 1.0 / ( FaradayConst * vol );
+  double B = 1.0 / ( VALENCE* FaradayConst * vol );
   vSetB( e, B );
 }
 

python/rdesigneur/rdesigneur.py

@@ -1249,7 +1249,6 @@ def _assignComptNamesFromKkit( self ):
                 comptList[0].name = 'dend'
             return comptList
         if not self._isModelFromKkit():
-            print( "Not isModelfromKkit" )
             return comptList
         sortedComptList = sorted( comptList, key=lambda x: -x.volume )
         if self.addSomaChemCompt:
@@ -1393,7 +1392,11 @@ def _configureSolvers( self ) :
 
     def _loadChem( self, fname, chemName ):
         chem = moose.Neutral( '/library/' + chemName )
-        modelId = moose.loadModel( fname, chem.path, 'ee' )
+        pre, ext = os.path.splitext( fname )
+        if ext == '.xml' or ext == '.sbml':
+            modelId = moose.mooseReadSBML( fname, chem.path )
+        else:
+            modelId = moose.loadModel( fname, chem.path, 'ee' )
         comptlist = moose.wildcardFind( chem.path + '/#[ISA=ChemCompt]' )
         if len( comptlist ) == 0:
             print("loadChem: No compartment found in file: ", fname)