Merge pull request #50 from ReactionMechanismGenerator/symmetry

Updated symmetry calculations

autotst/reactionTest.py

@@ -245,7 +245,16 @@ def test_ase_molecule(self):
     def test_symmetry_number(self):
         self.assertEquals(self.ts.symmetry_number, 1)
         self.assertEquals(self.ts2.symmetry_number, 1)
-        os.remove("./CC.[O]O.symm")
+
+        reactions_to_test = {
+            "[CH3]+[OH]_C+[O]" : 3,
+            # TODO add other reactions here
+        }
+        for reaction_string, expected_symmetry in reactions_to_test.items():
+            rxn = Reaction(reaction_string)
+            rxn.get_labeled_reaction() 
+            ts = rxn.ts["forward"][0]
+            self.assertEquals(ts.symmetry_number, expected_symmetry) 
 
     def test_bounds_matrix(self):
 

autotst/species.py

@@ -1062,28 +1062,16 @@ def set_chirality(self, chiral_center_index, stero="R"):
         return self
 
     def calculate_symmetry_number(self):
-        from rmgpy.qm.symmetry import PointGroupCalculator
-        from rmgpy.qm.qmdata import QMData
-
-        atom_numbers = self.ase_molecule.get_atomic_numbers()
-        coordinates = self.ase_molecule.get_positions()
-
-        qmdata = QMData(
-            groundStateDegeneracy=1,  # Only needed to check if valid QMData
-            numberOfAtoms=len(atom_numbers),
-            atomicNumbers=atom_numbers,
-            atomCoords=(coordinates, str('angstrom')),
-            energy=(0.0, str('kcal/mol'))  # Only needed to avoid error
-        )
-        settings = type(str(''), (), dict(symmetryPath=str(
-            'symmetry'), scratchDirectory="."))()  # Creates anonymous class
-        pgc = PointGroupCalculator(settings, self.smiles, qmdata)
-        pg = pgc.calculate()
-        #os.remove("{}.symm".format(self.smiles))
-
-        if pg is not None:
-            symmetry_number = pg.symmetry_number
-        else:
-            symmetry_number = 1
 
-        return symmetry_number
+        numbers = self.ase_molecule.numbers
+        positions = self.ase_molecule.positions
+
+        mol = RMGMolecule()
+        mol.from_xyz(numbers, positions)
+        try:
+            species = RMGSpecies(molecule=[mol])
+            self._symmetry_number = species.get_symmetry_number()
+        except ValueError:
+            self._symmetry_number = mol.get_symmetry_number() 
+
+        return self._symmetry_number

autotst/speciesTest.py

@@ -94,8 +94,11 @@ def test_get_geometries(self):
         self.assertIsInstance(geometries[3],list)
         self.assertIsInstance(geometries[4],list)
     def test_calculate_symmetry_number(self):
-        self.assertTrue(self.conformer.calculate_symmetry_number() in [1,2])
-        os.remove("./CC.symm")
+        species_to_test = {
+            "CC" : 18.0,
+
+        }
+        self.assertEquals(self.conformer.calculate_symmetry_number(), 18.0)
     def test_get_xyz_block(self):
         xyz_block = self.conformer.get_xyz_block()
         positions = self.conformer.ase_molecule.arrays["positions"]