Fixed Fragment test

The `Fragment` class is now a subclass of
`Molecule`. As such, some if statements for
checking atom charges no longer work for Fragments
since CuttingLabels don't have defined charges.

These if statements were modified such that charge
checks for `Fragments` ignore CuttingLabels.

Author: ssun30

rmgpy/data/kinetics/family.py

@@ -1520,9 +1520,10 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True, relabel_a
             # (families with charged substances), the charge of structures will be updated
             if isinstance(struct, Molecule):
                 struct.update_charge()
-                struct.update(sort_atoms=not self.save_order)
-            elif isinstance(struct, Fragment):
-                struct.update()
+                if isinstance(struct, Fragment):
+                    struct.update()
+                else:
+                    struct.update(sort_atoms=not self.save_order)
             elif isinstance(struct, Group):
                 is_molecule = False
                 struct.reset_ring_membership()

rmgpy/molecule/group.py

@@ -44,6 +44,7 @@
 from rmgpy.molecule.atomtype import ATOMTYPES, allElements, nonSpecifics, get_features, AtomType
 from rmgpy.molecule.element import PeriodicSystem
 from rmgpy.molecule.graph import Vertex, Edge, Graph
+from rmgpy.molecule.fragment import CuttingLabel
 
 
 ################################################################################

rmgpy/molecule/molecule.py

@@ -58,6 +58,7 @@
 from rmgpy.molecule.graph import Vertex, Edge, Graph, get_vertex_connectivity_value
 from rmgpy.molecule.kekulize import kekulize
 from rmgpy.molecule.pathfinder import find_shortest_path
+from rmgpy.molecule.fragment import CuttingLabel
 
 ################################################################################
 

rmgpy/reaction.py

@@ -1440,33 +1440,31 @@ def is_balanced(self):
                     if not isinstance(atom, CuttingLabel):
                         reactants_net_charge += atom.charge
                         reactant_elements[atom.element] += 1
-            elif isinstance(reactant, Molecule):
-                molecule = reactant
-                for atom in molecule.atoms:
-                    reactants_net_charge += atom.charge
-                    reactant_elements[atom.element] += 1
             elif isinstance(reactant, Fragment):
                 for atom in reactant.atoms:
                     if not isinstance(atom, CuttingLabel):
                         reactants_net_charge += atom.charge
                         reactant_elements[atom.element] += 1
+            elif isinstance(reactant, Molecule):
+                for atom in reactant.atoms:
+                    reactants_net_charge += atom.charge
+                    reactant_elements[atom.element] += 1
         for product in self.products:
             if isinstance(product, Species):
                 molecule = product.molecule[0]
                 for atom in molecule.atoms:
                     if not isinstance(atom, CuttingLabel):
                         products_net_charge += atom.charge
                         product_elements[atom.element] += 1
-            elif isinstance(product, Molecule):
-                molecule = product
-                for atom in molecule.atoms:
-                    products_net_charge += atom.charge
-                    product_elements[atom.element] += 1
             elif isinstance(product, Fragment):
                 for atom in product.atoms:
                     if not isinstance(atom, CuttingLabel):
                         products_net_charge += atom.charge
                         product_elements[atom.element] += 1
+            elif isinstance(product, Molecule):
+                for atom in product.atoms:
+                    products_net_charge += atom.charge
+                    product_elements[atom.element] += 1
 
         for element in element_list:
             if reactant_elements[element] != product_elements[element]: