Merge pull request #870 from StochSS/fix_869

Fixing homo-dimer bimolecular propensity function
StochSS · Oct 5, 2022 · 71cd8d1 · 71cd8d1
2 parents cb08a9d + 6ffd93c
commit 71cd8d1
Show file tree

Hide file tree

Showing 3 changed files with 251 additions and 3 deletions.
diff --git a/examples/Advanced_Features/Bimolecular_reactions.ipynb b/examples/Advanced_Features/Bimolecular_reactions.ipynb
diff --git a/gillespy2/core/reaction.py b/gillespy2/core/reaction.py
@@ -295,7 +295,7 @@ def _create_mass_action(self):
                 reactant = reactant.name
             # Case 1: 2X -> Y
             if stoichiometry == 2:
-                propensity_function = f"0.5 * {propensity_function} * {reactant} * ({reactant} - 1) / vol"
+                propensity_function = f"{propensity_function} * {reactant} * ({reactant} - 1) / vol"
                 ode_propensity_function += f" * {reactant} * {reactant}"
             else:
                 # Case 3: X1, X2 -> Y;

diff --git a/test/unit_tests/test_reaction.py b/test/unit_tests/test_reaction.py
@@ -405,7 +405,7 @@ def test__create_mass_action__2X_to_Y(self):
         self.valid_ma_reaction.reactants = {"X": 2}
         self.valid_ma_reaction.products = {"Y": 1}
         self.valid_ma_reaction._create_mass_action()
-        self.assertEqual(self.valid_ma_reaction.propensity_function, "((((0.5*k1)*X)*(X-1))/vol)")
+        self.assertEqual(self.valid_ma_reaction.propensity_function, "(((k1*X)*(X-1))/vol)")
         self.assertEqual(self.valid_ma_reaction.ode_propensity_function, "((k1*X)*X)")
 
     def test__create_mass_action__species_obj_reactant(self):
@@ -536,7 +536,7 @@ def test_add_reactant__massaction_reaction_stoich_0_to_2(self):
         self.valid_ma_reaction.add_reactant("X", 2)
         self.assertIn("X", self.valid_ma_reaction.reactants)
         self.assertEqual(self.valid_ma_reaction.reactants["X"], 2)
-        self.assertEqual(self.valid_ma_reaction.propensity_function, "((((0.5*k1)*X)*(X-1))/vol)")
+        self.assertEqual(self.valid_ma_reaction.propensity_function, "(((k1*X)*(X-1))/vol)")
         self.assertEqual(self.valid_ma_reaction.ode_propensity_function, "((k1*X)*X)")
 
     def test_add_reactant__invalid_species(self):