Tests: converter order_xyz_by_atom_map()

Author: alongd

arc/species/converter_test.py

@@ -4558,6 +4558,45 @@ def test_check_isomorphism(self):
         mol2 = Molecule(smiles='[N-]=[N+]=O')
         self.assertTrue(converter.check_isomorphism(mol1, mol2))
 
+    def test_order_xyz_by_atom_map(self):
+        """Test ordering xyz by atom map"""
+        xyz = {'symbols': ('C', 'H', 'H', 'H', 'H'),
+               'isotopes': (12, 1, 1, 1, 1),
+               'coords': ((0.0, 0.0, 0.0),
+                          (0.6300326, 0.6300326, 0.6300326),
+                          (-0.6300326, -0.6300326, 0.6300326),
+                          (-0.6300326, 0.6300326, -0.6300326),
+                          (0.6300326, -0.6300326, -0.6300326))}
+        atom_map = [4, 3, 1, 2, 0]
+        ordered_xyz = converter.order_xyz_by_atom_map(xyz, atom_map)
+        expected_xyz = {'symbols': ('H', 'H', 'H', 'H', 'C'),
+                        'isotopes': (1, 1, 1, 1, 12),
+                        'coords': ((0.6300326, -0.6300326, -0.6300326),
+                                   (-0.6300326, 0.6300326, -0.6300326),
+                                   (0.6300326, 0.6300326, 0.6300326),
+                                   (-0.6300326, -0.6300326, 0.6300326),
+                                   (0.0, 0.0, 0.0))}
+        self.assertEqual(ordered_xyz, expected_xyz)
+
+        xyz = {'symbols': ('C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
+               'isotopes': (12, 12, 12, 1, 1, 1, 1, 1, 1, 1),
+               'coords': ((-0.4073569, -0.74240205, -0.34312948), (0.38155377, -0.25604705, 0.82450968),
+                          (0.54634593, 1.25448345, 0.81064511), (0.00637731, -1.58836501, -0.88041673),
+                          (-0.98617584, -0.01198912, -0.89732723), (-1.29710684, -1.2909234, 0.08598983),
+                          (1.36955428, -0.72869684, 0.81102246), (1.06044877, 1.58846788, -0.09702437),
+                          (1.13774084, 1.57830484, 1.67308862), (-0.42424546, 1.75989927, 0.85794283))}
+        ordered_xyz = converter.order_xyz_by_atom_map(xyz, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
+        self.assertEqual(ordered_xyz, xyz)
+        expected_xyz = {'symbols': ('H', 'H', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'C'),
+                        'isotopes': (1, 1, 1, 1, 1, 1, 1, 12, 12, 12),
+                        'coords': ((-0.42424546, 1.75989927, 0.85794283), (1.13774084, 1.57830484, 1.67308862),
+                                   (1.06044877, 1.58846788, -0.09702437), (1.36955428, -0.72869684, 0.81102246),
+                                   (-1.29710684, -1.2909234, 0.08598983), (-0.98617584, -0.01198912, -0.89732723),
+                                   (0.00637731, -1.58836501, -0.88041673), (0.54634593, 1.25448345, 0.81064511),
+                                   (0.38155377, -0.25604705, 0.82450968), (-0.4073569, -0.74240205, -0.34312948))}
+        ordered_xyz = converter.order_xyz_by_atom_map(xyz, [9, 8, 7, 6, 5, 4, 3, 2, 1, 0])
+        self.assertEqual(ordered_xyz, expected_xyz)
+
     def test_cluster_confs_by_rmsd(self):
         nco_1 = {'symbols': ('C', 'H', 'H', 'O', 'H', 'N', 'H', 'H'),
                  'isotopes': (12, 1, 1, 16, 1, 14, 1, 1),