def test_atom_symmetry_number_ethane_with_deuterium_tritium(self):
"""
Test the Molecule.calculate_atom_symmetry_number() on CC(D)(T)
This is meant to test whether chirality is accounted for, which
should half the symmetry term.
The total number is 1.5 because the methyl group contributes *3 and
the chiral center contributes *0.5
"""
molecule = Molecule().from_adjacency_list("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 D u0 p0 c0 {1,S}
4 T u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
""")
symmetry_number = 1
for atom in molecule.atoms:
if not molecule.is_atom_in_cycle(atom):
symmetry_number *= calculate_atom_symmetry_number(
molecule, atom)
self.assertAlmostEqual(symmetry_number, 1.5)
def test_atom_symmetry_number_ethane(self):
"""
Test the Molecule.calculate_atom_symmetry_number() on CC
"""
molecule = Molecule().from_smiles('CC')
symmetry_number = 1
for atom in molecule.atoms:
if not molecule.is_atom_in_cycle(atom):
symmetry_number *= calculate_atom_symmetry_number(
molecule, atom)
self.assertEqual(symmetry_number, 9)
def test_atom_symmetry_number_allyl(self):
"""
Test the Molecule.calculate_atom_symmetry_number() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().from_smiles('[CH2]C=C')])
molecule = spc.get_resonance_hybrid()
symmetry_number = 1
for atom in molecule.atoms:
if not molecule.is_atom_in_cycle(atom):
symmetry_number *= calculate_atom_symmetry_number(
molecule, atom)
self.assertEqual(symmetry_number, 2)
def test_edge_carbon_atom_symmetry_number_allyl(self):
"""
Test the Molecule.calculate_atom_symmetry_number() for the edge carbons
on [CH2]C=C
"""
spc = Species(molecule=[Molecule().from_smiles('[CH2]C=C')])
molecule = spc.get_resonance_hybrid()
for atom in molecule.atoms:
if atom.symbol == 'C':
number_carbon_bonds = sum(
[1 for bond in atom.bonds if bond.symbol == 'C'])
if number_carbon_bonds == 1:
atom.label = 'edge'
symmetry_number = calculate_atom_symmetry_number(
molecule, atom)
self.assertEqual(symmetry_number, 1)
def test_middle_carbon_atom_symmetry_number_allyl_using_resonance_hybrid(
self):
"""
Test the Molecule.calculate_atom_symmetry_number() for the middle carbon
on [CH2]C=C using the resonance hybrid structure
"""
molecule = Molecule().from_smiles('[CH2]C=C')
species = Species(molecule=[molecule])
resonance_hybrid = species.get_resonance_hybrid()
for atom in resonance_hybrid.atoms:
if atom.symbol == 'C':
number_carbon_bonds = sum(
[1 for bond in atom.bonds if bond.symbol == 'C'])
if number_carbon_bonds == 2:
atom.label = 'center'
symmetry_number = calculate_atom_symmetry_number(
resonance_hybrid, atom)
self.assertEqual(symmetry_number, 2)
pass
def test_atom_symmetry_number_with_two_chiral_centers(self):
"""
Test the Molecule.calculate_atom_symmetry_number() on [CH2]CC([CH2])C(C)C=C
This is meant to test whether chirality is accounted for, which
should half the symmetry term.
The molecule has one methyl group (*3), two CH2dot groups (*2 each), and
two chiral centers (*0.5), leading to a total atom symmetry number of 3
"""
molecule = Molecule().from_adjacency_list("""
multiplicity 3
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {13,S} {14,S}
5 C u0 p0 c0 {4,S} {6,S} {9,S} {15,S}
6 C u1 p0 c0 {5,S} {7,S} {8,S}
7 H u0 p0 c0 {6,S}
8 H u0 p0 c0 {6,S}
9 C u0 p0 c0 {5,S} {10,S} {11,S} {16,S}
10 C u0 p0 c0 {9,S} {17,S} {18,S} {19,S}
11 C u0 p0 c0 {9,S} {12,D} {20,S}
12 C u0 p0 c0 {11,D} {21,S} {22,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
15 H u0 p0 c0 {5,S}
16 H u0 p0 c0 {9,S}
17 H u0 p0 c0 {10,S}
18 H u0 p0 c0 {10,S}
19 H u0 p0 c0 {10,S}
20 H u0 p0 c0 {11,S}
21 H u0 p0 c0 {12,S}
22 H u0 p0 c0 {12,S}
""")
symmetry_number = 1
for atom in molecule.atoms:
if not molecule.is_atom_in_cycle(atom):
symmetry_number *= calculate_atom_symmetry_number(
molecule, atom)
self.assertAlmostEqual(symmetry_number, 3)
