To rxn smiles (#729)

Added a feature to turn get a reaction SMILES from an ARCReaction.

arc/reaction.py

@@ -975,6 +975,25 @@ def copy_e0_values(self, other_rxn: Optional['ARCReaction']):
                     if spc.label == other_spc.label:
                         spc.e0 = spc.e0 or other_spc.e0
 
+    def get_rxn_smiles(self) -> Optional[str]:
+        """
+        returns the reaction smiles of the reaction.
+
+    Raises:
+        ValueError: If any of the species (reactants or products) has no SMILES (or could not be generated for some reason).
+
+    Returns: string
+        The reaction SMILES
+        """
+        reactants, products = self.get_reactants_and_products(arc=True, return_copies=True)
+        smiles_r = [reactant.mol.copy(deep=True).to_smiles() for reactant in reactants]
+        smiles_p = [product.mol.copy(deep=True).to_smiles() for product in products]
+        if not any(smiles_r) or not any(smiles_p):
+            raise ValueError(f"""Could not find smiles for one or more species
+                                 got: reactants: {smiles_r}
+                                      products: {smiles_p}""")
+        return ".".join(smiles_r)+">>"+".".join(smiles_p)
+
 
 def remove_dup_species(species_list: List[ARCSpecies]) -> List[ARCSpecies]:
     """

arc/reaction_test.py

@@ -2020,6 +2020,20 @@ def test_load_ts_xyz_user_guess_from_files(self):
         self.assertEqual(len(arc_object.reactions[0].ts_species.ts_guesses), 2)
         self.assertEqual(len(arc_object.reactions[0].ts_species.ts_guesses[1].initial_xyz['symbols']), 19)
 
+    def test_get_rxn_smiles(self):
+        """Tests the get_rxn_smiles method"""
+        self.assertEqual(self.rxn1.get_rxn_smiles(), "C.[OH]>>[CH3].O")
+        self.assertEqual(self.rxn2.get_rxn_smiles(), "C[CH2].[OH]>>C=C.O")
+        self.assertEqual(self.rxn3.get_rxn_smiles(), "CC[NH]>>[CH2]CN")
+        self.assertEqual(self.rxn4.get_rxn_smiles(), "[NH2].[NH]N>>N.[N]N")
+        self.assertEqual(self.rxn5.get_rxn_smiles(), "[NH2].[NH2]>>[NH].N")
+        self.assertEqual(self.rxn6.get_rxn_smiles(), "[NH2].[NH]N>>N.[N-]=[NH2+]")
+        self.assertEqual(self.rxn7.get_rxn_smiles(), "[NH2].[NH]N>>N.[N]N")
+        self.assertEqual(self.rxn8.get_rxn_smiles(), "C.[OH]>>[CH3].O")
+        self.assertEqual(self.rxn9.get_rxn_smiles(), "NCO[O]>>C=N.[O]O")
+        self.assertEqual(self.rxn10.get_rxn_smiles(), "N=O.[O-][N+]=O>>[O-][NH+]=O.[N]=O")
+        self.assertEqual(self.rxn11.get_rxn_smiles(), "C[CH]C>>[CH2]CC")
+
     @classmethod
     def tearDownClass(cls):
         """A function that is run ONCE after all unit tests in this class."""