Test: cut_species_based_on_atom_indices

arc/mapping/engine_test.py

@@ -601,15 +601,18 @@ def test_label_species_atoms(self):
                 self.assertEqual(atom.label,str(index))
                 index +=1
 
-    def test_cut_species_for_mapping(self):
+    def test_cut_species_based_on_atom_indices(self):
         """test the cut_species_for_mapping function"""
         rxn_1_test = ARCReaction(r_species=[self.r_1, self.r_2], p_species=[self.p_1, self.p_2])
         rxn_1_test.determine_family(self.db)
-        reactants, products, loc_r, loc_p = prepare_reactants_and_products_for_scissors(rxn_1_test,
-                                                                                        self.r_label_dict_rxn_1,
-                                                                                        self.p_label_dict_rxn_1)
-        r_cuts = cut_species_for_mapping(reactants, loc_r)
-        p_cuts = cut_species_for_mapping(products, loc_p)
+        reactants, products = copy_species_list_for_mapping(rxn_1_test.r_species), copy_species_list_for_mapping(rxn_1_test.p_species)
+        label_species_atoms(reactants), label_species_atoms(products)
+
+        r_bdes, p_bdes = find_all_bdes(rxn_1_test, self.r_label_dict_rxn_1, True), find_all_bdes(rxn_1_test, self.p_label_dict_rxn_1, False)
+
+        r_cuts = cut_species_based_on_atom_indices(reactants, r_bdes)
+        p_cuts = cut_species_based_on_atom_indices(products, p_bdes)
+
 
         self.assertIn("C[CH]C", [r_cut.mol.copy(deep=True).smiles for r_cut in r_cuts])
         self.assertIn("[F]", [r_cut.mol.copy(deep=True).smiles for r_cut in r_cuts])
@@ -621,21 +624,24 @@ def test_cut_species_for_mapping(self):
         spc = ARCSpecies(label="test", smiles="CNC", bdes = [(1, 2), (2, 3)])
         for i, a in enumerate(spc.mol.atoms):
             a.label=str(i)
-        cuts = cut_species_for_mapping([spc], [2])
+        cuts = cut_species_based_on_atom_indices([spc], [(1, 2), (2, 3)])
         self.assertEqual(len(cuts), 3)
         for cut in cuts:
             self.assertTrue(any([cut.mol.copy(deep=True).is_isomorphic(ARCSpecies(label="1", smiles="[CH3]").mol),
                                  cut.mol.copy(deep=True).is_isomorphic(ARCSpecies(label="2", smiles="[NH]").mol)]))
 
-        cuts =  cut_species_for_mapping([ARCSpecies(label="H2", smiles="[H][H]", bdes=[(1, 2)])], [1])
+        h2 = ARCSpecies(label="H2", smiles="[H][H]")
+        label_species_atoms([h2])
+
+        cuts =  cut_species_based_on_atom_indices([h2], [(1, 2)])
         self.assertEqual(len(cuts), 2)
         for cut in cuts:
             self.assertEqual(cut.get_xyz()["symbols"], ('H',))
-
-    def test_multiple_cut_on_species(self):
-        """test the multiple_cut_on_species function"""
-        spc = ARCSpecies(label="test", smiles="NCN", bdes = [(1, 2), (2, 3)])
-        for i, a in enumerate(spc.mol.atoms):
+        
+        spcs = [ARCSpecies(label="r", smiles = 'O=C(O)CCF')]
+        label_species_atoms(spcs)
+        cuts = cut_species_based_on_atom_indices(spcs, [(6, 5), (4, 2), (3, 7)])
+        self.assertEqual(len(cuts), 4)
             a.label=str(i)
         spc.final_xyz = spc.get_xyz()
         cuts = multiple_cut_on_species(spc, spc.bdes)