From d4f146371a457dabf0142eaa240af267a6f2331e Mon Sep 17 00:00:00 2001
From: ssun30 <sun.su@northeastern.edu>
Date: Fri, 4 Oct 2024 16:27:19 -0400
Subject: [PATCH] Fixed Fragment test failure

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, and
will skip charge checks for `Molecules` if the
species is an instance `Fragments`.
---
 rmgpy/data/kinetics/family.py |  5 ++---
 rmgpy/reaction.py             | 20 ++++++++++----------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/rmgpy/data/kinetics/family.py b/rmgpy/data/kinetics/family.py
index 8ba433e34a..291e639380 100644
--- a/rmgpy/data/kinetics/family.py
+++ b/rmgpy/data/kinetics/family.py
@@ -1519,10 +1519,9 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True, relabel_a
             # If product structures are Group objects and the reaction is in certain families
             # (families with charged substances), the charge of structures will be updated
             if isinstance(struct, Molecule):
-                struct.update_charge()
+                if not isinstance(struct, Fragment):
+                    struct.update_charge()
                 struct.update(sort_atoms=not self.save_order)
-            elif isinstance(struct, Fragment):
-                struct.update()
             elif isinstance(struct, Group):
                 is_molecule = False
                 struct.reset_ring_membership()
diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index 90471acc19..80be78e154 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -1440,16 +1440,16 @@ 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):
+                molecule = reactant
+                for atom in molecule.atoms:
+                    reactants_net_charge += atom.charge
+                    reactant_elements[atom.element] += 1
         for product in self.products:
             if isinstance(product, Species):
                 molecule = product.molecule[0]
@@ -1457,16 +1457,16 @@ def is_balanced(self):
                     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):
+                molecule = product
+                for atom in molecule.atoms:
+                    products_net_charge += atom.charge
+                    product_elements[atom.element] += 1
 
         for element in element_list:
             if reactant_elements[element] != product_elements[element]: