diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index a8ae13f3d3..477e29cc96 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -1447,7 +1447,7 @@ def is_balanced(self):
         from rmgpy.molecule.element import element_list
         from rmgpy.molecule.fragment import CuttingLabel, Fragment
 
-        cython.declare(reactant_elements=dict, product_elements=dict, molecule=Graph, atom=Vertex, element=Element,
+        cython.declare(reactant_elements=dict, product_elements=dict, molecule=Molecule, atom=Atom, element=Element,
                        reactants_net_charge=cython.int, products_net_charge=cython.int)
 
         reactant_elements = {}
diff --git a/rmgpy/rmg/model.py b/rmgpy/rmg/model.py
index f937ac8842..225c8f5539 100644
--- a/rmgpy/rmg/model.py
+++ b/rmgpy/rmg/model.py
@@ -365,10 +365,11 @@ def make_new_species(self, object, label="", reactive=True, check_existing=True,
         spec.molecular_weight = Quantity(spec.molecule[0].get_molecular_weight() * 1000.0, "amu")
 
         if generate_thermo:
-            self.generate_thermo(spec)
+            # Rename from thermo library label only if no user-provided label exists yet.
+            self.generate_thermo(spec, rename=not bool(spec.label))
 
         # If the species still does not have a label, set initial label as the SMILES
-        # This may change later after getting thermo in self.generate_thermo()
+        # (applies when generate_thermo is False, or when no library match was found)
         if not spec.label:
             spec.label = spec.smiles