diff --git a/bng/__init__.py b/bng/__init__.py
index 61531da..77abb25 100644
--- a/bng/__init__.py
+++ b/bng/__init__.py
@@ -38,14 +38,16 @@ def execute(self, context):
         if hasattr(external_operators.accessFile,"info"):
             del external_operators.accessFile.info
 
-        if('.bngl') in self.filepath:
+        is_file_xml = self.filepath.endswith('.xml')
+	
+        if self.filepath.endswith('.bngl'):
             bngfilepath = self.filepath         # bngl file path
             external_operators.filePath=findCellBlenderDirectory()+'bng{0}'.format(os.sep) + self.filepath.split(os.sep)[-1]
             print ( "Calling bng_operators.execute_bionetgen("+bngfilepath+")" )
             bng_operators.execute_bionetgen(self.filepath,context)
             print ( "Back from bng_operators.execute_bionetgen("+bngfilepath+")" )
 
-        elif('.xml') in self.filepath:
+        elif is_file_xml:
             sbmlfilepath = self.filepath
             external_operators.filePath = sbmlfilepath
             # sbml file path
@@ -67,7 +69,7 @@ def execute(self, context):
         print ( "Loading release sites from external model..." )
         bpy.ops.external.release_site_add()
         print ( "Done Loading external model" )
-        if ('.xml') in self.filepath:
+        if is_file_xml:
             #TODO:this is sbml only until we add this information on the bng side
             print("Loading reaction output ...")
             bpy.ops.external.reaction_output_add()
@@ -78,9 +80,7 @@ def execute(self, context):
         ###  THIS ENTIRE SECTION IS A QUICK HACK TO HANDLE XML IMPORTING
         ###
         ###
-        if ('.xml' in self.filepath) and ('mcell' in context.scene):
-            # Note that searching for ".xml" in the filepath may not be reliable since it should end with .xml.
-            # Keeping the same for now.
+        if is_file_xml and self.add_to_model_objects and ('mcell' in context.scene):
             print ( "Pulling object structure from XML file: " + self.filepath )
             
             mcell = context.scene.mcell
diff --git a/bng/sbml2json.py b/bng/sbml2json.py
index 2d2655d..04b67cf 100644
--- a/bng/sbml2json.py
+++ b/bng/sbml2json.py
@@ -393,10 +393,10 @@ def getInstanceRate(self,math,compartmentList, reversible,rReactant,rProduct):
             else:
                 rateL, nl = self.removeFactorFromMath(math, rReactant,
                                                       rProduct)
-                rateL = "if({0} >= 0 ,{0},0)".format(rateL)
+                # rateL = "if({0} >= 0 ,{0},0)".format(rateL)
                 rateR, nr = self.removeFactorFromMath(math, rReactant,
                                                       rProduct)
-                rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
+                # rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
                 nl, nr = 1,1
         else:
             rateL, nl = (self.removeFactorFromMath(math.deepCopy(),
@@ -426,8 +426,8 @@ def removeFactorFromMath(self, math, reactants, products):
         #remainderPatterns = [x[0] for x in reactants]
         math = self.getPrunnedTree(math,remainderPatterns)
         rateR = libsbml.formulaToString(math) 
-        for element in remainderPatterns:
-            rateR = 'if({0} >0,({1})/{0} ,0)'.format(element,rateR)
+        # for element in remainderPatterns:
+            # rateR = 'if({0} >0,({1})/{0} ,0)'.format(element,rateR)
         if highStoichoiMetryFactor != 1:
             rateR = '{0}*{1}'.format(rateR, int(highStoichoiMetryFactor))
 
@@ -494,7 +494,7 @@ def getContained(compartmentList,container):
             math = kineticLaw.getMath()
             reversible = reaction.getReversible()
                 
-            rateL, rateR = self.getInstanceRate(math,compartmentList.keys(),reversible,rReactant,rProduct)
+            rateL, rateR = self.getInstanceRate(math,list(compartmentList.keys()),reversible,rReactant,rProduct)
             #finalReactant = [x[0]]    
             #testing whether we have volume-surface interactions
             rcList = []
@@ -620,7 +620,7 @@ def getContained(compartmentList,container):
                 tmpR['reactants'] = ' + '.join(prdList)
                 if flagR:
                     virtualReaction= {}
-                    virtualReaction['rxn_name'] =  tmpL['rxn_name']
+                    virtualReaction['rxn_name'] =  tmpR['rxn_name']
                     tmpR.pop('rxn_name')
                     tmpR['products'] = '{0}_{1}_{2}'.format(product[0][0],reactant[0][2],reactant[0][0])
                     virtualReaction['reactants'] = tmpR['products']