Fix reaction degeneracy bug with keep_isomorphic argument

In certain situations, we would call ensure_species with
keep_isomorphic=False, which would ultimately result in wrong
degeneracy values.

This fixes that oversight and makes sure that keep_isomorphic=True
when generating reactions.

A unit test is also added.

rmgpy/data/kinetics/common.py

@@ -198,7 +198,7 @@ def ensure_independent_atom_ids(input_species, resonance=True):
     Modifies the list in place (replacing :class:`Molecule` with :class:`Species`).
     Returns None.
     """
-    ensure_species(input_species, resonance=resonance)
+    ensure_species(input_species, resonance=resonance, keep_isomorphic=True)
     # Method to check that all species' atom ids are different
     def independent_ids():
         num_atoms = 0

rmgpy/data/kinetics/kineticsTest.py

@@ -590,6 +590,19 @@ def test_degeneracy_multiple_resonance_different_template(self):
 
         self.assertFalse(reaction_list[0].duplicate)
 
+    def test_degeneracy_resonance_keep_isomorphic(self):
+        """Test that we get the correct degeneracy for [CH2]C=C[CH2] + [H].
+
+        Incorrect results would be obtained if isomorphic resonance structures are not kept."""
+        family_label = 'R_Recombination'
+        reactants = ['[CH2]C=C[CH2]', '[OH]']
+        products = ['[CH2]C(O)C=C']
+
+        correct_rxn_num = 1
+        correct_degeneracy = {2}
+
+        self.assert_correct_reaction_degeneracy(reactants, correct_rxn_num, correct_degeneracy, family_label, products)
+
 
 class TestKineticsCommentsParsing(unittest.TestCase):