Added Cl and Si to generatePairs() in reaction.py

Author: alongd

rmgpy/reaction.py

@@ -916,15 +916,19 @@ def generatePairs(self):
             productOxygens    = [sum([1 for atom in  product.molecule[0].atoms if atom.isOxygen()])   for product  in products ]
             reactantNitrogens = [sum([1 for atom in reactant.molecule[0].atoms if atom.isNitrogen()]) for reactant in reactants]
             productNitrogens  = [sum([1 for atom in  product.molecule[0].atoms if atom.isNitrogen()]) for product  in products ]
+            reactantSilicons  = [sum([1 for atom in reactant.molecule[0].atoms if atom.isSilicon()])  for reactant in reactants]
+            productSilicons   = [sum([1 for atom in  product.molecule[0].atoms if atom.isSilicon()])  for product  in products ]
             reactantSulfurs   = [sum([1 for atom in reactant.molecule[0].atoms if atom.isSulfur()])   for reactant in reactants]
             productSulfurs    = [sum([1 for atom in  product.molecule[0].atoms if atom.isSulfur()])   for product  in products ]
+            reactantChlorines = [sum([1 for atom in reactant.molecule[0].atoms if atom.isChlorine()]) for reactant in reactants]
+            productChlorines  = [sum([1 for atom in  product.molecule[0].atoms if atom.isChlorine()]) for product  in products ]
 
             # Sort the reactants and products by C/O/N/S numbers
-            reactants = [(carbon, oxygen, nitrogen, sulfur, reactant) for carbon, oxygen, nitrogen, sulfur, reactant
-                         in zip(reactantCarbons,reactantOxygens,reactantNitrogens,reactantSulfurs,reactants)]
+            reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant
+                         in zip(reactantCarbons,reactantOxygens,reactantNitrogens,reactantSilicons,reactantSulfurs,reactantChlorines,reactants)]
             reactants.sort()
-            products = [(carbon, oxygen, nitrogen, sulfur, product) for carbon, oxygen, nitrogen, sulfur, product
-                        in zip(productCarbons,productOxygens,productNitrogens,productSulfurs,products)]
+            products = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant
+                        in zip(productCarbons,productOxygens,productNitrogens,productSilicons,productSulfurs,productChlorines,products)]
             products.sort()
 
             while len(reactants) > 1 and len(products) > 1: