added halogen abstraction families to species cases in family.py

Author: davidfarinajr

rmgpy/data/kinetics/family.py

@@ -1430,7 +1430,7 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True, relabel_a
                 if atom.label != '':
                     atom_labels[atom.label] = atom
 
-            if label == 'h_abstraction':
+            if label in ('h_abstraction','f_abstraction','cl_abstraction','br_abstraction'):
                 # '*2' is the H that migrates
                 # it moves from '*1' to '*3'
                 atom_labels['*1'].label = '*3'
@@ -2393,7 +2393,7 @@ def get_reaction_pairs(self, reaction):
             for reactant in reaction.reactants:
                 for product in reaction.products:
                     pairs.append([reactant, product])
-        elif self.label.lower() == 'h_abstraction':
+        elif self.label.lower() in ('h_abstraction','f_abstraction','cl_abstraction','br_abstraction'):
             # Hardcoding for hydrogen abstraction: pair the reactant containing
             # *1 with the product containing *3 and vice versa
             assert len(reaction.reactants) == len(reaction.products) == 2