Tests: original mol in converter.molecules_from_xyz()

ReactionMechanismGenerator · Oct 28, 2024 · a7d2c7e · a7d2c7e
1 parent 8cddbe2
commit a7d2c7e
Showing 1 changed file with 22 additions and 0 deletions.
diff --git a/arc/species/converter_test.py b/arc/species/converter_test.py
@@ -3370,6 +3370,28 @@ def test_molecules_from_xyz(self):
         self.assertEqual(b_mol.multiplicity, 1)
         self.assertFalse(any(atom.radical_electrons for atom in b_mol.atoms))
 
+        c2h5no2_xyz = """O                  0.62193295    1.59121319   -0.58381518
+                         N                  0.43574593    0.41740669    0.07732982
+                         O                  1.34135576   -0.35713755    0.18815532
+                         C                 -0.87783860    0.10001361    0.65582554
+                         C                 -1.73002357   -0.64880063   -0.38564362
+                         H                 -1.37248469    1.00642547    0.93625873
+                         H                 -0.74723653   -0.51714586    1.52009245
+                         H                 -1.23537748   -1.55521250   -0.66607681
+                         H                 -2.68617014   -0.87982825    0.03543830
+                         H                 -1.86062564   -0.03164117   -1.24991054"""
+        original_molecule = Molecule(smiles='CC[N+](=O)[O-]')
+        s_mol, b_mol = converter.molecules_from_xyz(converter.str_to_xyz(c2h5no2_xyz),
+                                                    multiplicity=1,
+                                                    charge=0,
+                                                    original_molecule=original_molecule,
+                                                    )
+        self.assertEqual(s_mol.get_net_charge(), 0)
+        self.assertEqual(b_mol.get_net_charge(), 0)
+        self.assertIn('[N+]', b_mol.to_smiles())
+        self.assertIn('[O-]', b_mol.to_smiles())
+        self.assertIn('=O', b_mol.to_smiles())
+
     def test_unsorted_xyz_mol_from_xyz(self):
         """Test atom order conservation when xyz isn't sorted with heavy atoms first"""
         n3h5 = ARCSpecies(label='N3H5', xyz=self.xyz8['str'], smiles='NNN')