fixup! added electronLabel for rxn family and recipe

rmgpy/data/kinetics/family.py

@@ -227,7 +227,6 @@ class ReactionRecipe(object):
 
     def __init__(self, actions=None):
         self.actions = actions or []
-        self.electron_label = None
 
     def add_action(self, action):
         """
@@ -359,8 +358,7 @@ def _apply(self, struct, forward, unique):
                                 electron.lone_pairs = 0
                             elif isinstance(struct, Group):
                                 electron = GroupAtom(atomtype=['e'])
-                                #struct = struct.merge(Group(atoms=[GroupAtom(atomtype=['e'])]))
-                            electron.label = self.electron_label
+                            electron.label = '*'
                             struct.add_atom(electron)
 
             elif action[0] in ['LOSE_PAIR', 'GAIN_PAIR']:
@@ -681,7 +679,6 @@ def load(self, path, local_context=None, global_context=None, depository_labels=
         local_context['reverseMap'] = None
         local_context['reactantNum'] = None
         local_context['productNum'] = None
-        local_context['electronLabel'] = None
         local_context['autoGenerated'] = False
         self.groups = KineticsGroups(label='{0}/groups'.format(self.label))
         logging.debug("Loading kinetics family groups from {0}".format(os.path.join(path, 'groups.py')))
@@ -693,7 +690,6 @@ def load(self, path, local_context=None, global_context=None, depository_labels=
 
         self.reactant_num = local_context.get('reactantNum', None)
         self.product_num = local_context.get('productNum', None)
-        self.electron_label = local_context.get('electronLabel', None)
 
         self.auto_generated = local_context.get('autoGenerated', False)
 
@@ -708,7 +704,6 @@ def load(self, path, local_context=None, global_context=None, depository_labels=
             self.forward_template.products = self.forward_template.reactants[:]
             self.reverse_template = None
             self.reverse_recipe = self.forward_recipe.get_reverse()
-            self.reverse_recipe.electron_label = self.electron_label
         else:
             self.reverse = local_context.get('reverse', None)
             self.reversible = True if local_context.get('reversible', None) is None else local_context.get('reversible', None)
@@ -717,11 +712,9 @@ def load(self, path, local_context=None, global_context=None, depository_labels=
                 self.reverse_template = Reaction(reactants=self.forward_template.products,
                                                  products=self.forward_template.reactants)
                 self.reverse_recipe = self.forward_recipe.get_reverse()
-                self.reverse_recipe.electron_label = self.electron_label
                 if self.reverse is None:
                     self.reverse = '{0}_reverse'.format(self.label)
 
-        self.forward_recipe.electron_label = self.electron_label
         self.rules = KineticsRules(label='{0}/rules'.format(self.label))
         logging.debug("Loading kinetics family rules from {0}".format(os.path.join(path, 'rules.py')))
         self.rules.load(os.path.join(path, 'rules.py'), local_context, global_context)
@@ -986,8 +979,6 @@ def save_groups(self, path):
             f.write('reactantNum = {0}\n\n'.format(self.reactant_num))
         if self.product_num is not None:
             f.write('productNum = {0}\n\n'.format(self.product_num))
-        if self.electron_label is not None:
-            f.write('electronLabel = "{0}"\n\n'.format(self.electron_label))
 
         if self.auto_generated is not None:
             f.write('autoGenerated = {0}\n\n'.format(self.auto_generated))
@@ -1580,10 +1571,14 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True):
             lowest_labels = []
             for struct in product_structures:
                 # Extract digits from labels and convert others (e.g., "*") to empty strings
-                labels = [''.join(c for c in label if c.isdigit()) for label in struct.get_all_labeled_atoms().keys()]
-                # Convert digits to integers and remove empty strings
-                labels = [int(label) for label in labels if label]
-                lowest_labels.append(min(labels))
+                labels = [label for label in struct.get_all_labeled_atoms().keys()]
+                if labels == ['*']:
+                    lowest_labels.append(0)
+                else:
+                    labels = [''.join(c for c in label if c.isdigit()) for label in labels]
+                    # Convert digits to integers and remove empty strings
+                    labels = [int(label) for label in labels if label]
+                    lowest_labels.append(min(labels))
             product_structures = [s for _, s in sorted(zip(lowest_labels, product_structures))]
 
         # Return the product structures

rmgpy/test_data/testing_database/kinetics/families/Surface_Proton_Electron_Reduction_Alpha/groups.py

@@ -6,7 +6,7 @@
 longDesc = u"""
 
    *1                        *1-*3H
-   ||  + *3H+ + *4e-  ---->   |
+   ||  + *3H+ + *e-  ---->   |
   ~*2~                      ~*2~~
 
 The rate, which should be in mol/m2/s,
@@ -20,7 +20,6 @@
 
 reactantNum = 3
 productNum = 1
-electronLabel = '*4'
 
 recipe(actions=[
     ['LOSE_CHARGE', '*3', 1],
@@ -54,7 +53,7 @@
     label = "Electron",
     group =
 """
-1 *4 e u0 p0 c-1
+1 * e u0 p0 c-1
 """,
     kinetics = None,
 )