def test_generate_resonance_structures2(self):
adj = """1 C u0 p0 c0 {2,D} {10,S} {11,S}
2 C u0 p0 c0 {1,D} {3,S} {12,S}
3 C u0 p0 c0 {2,S} {4,D} {13,S}
4 C u0 p0 c0 {3,D} {5,S} {9,S}
5 C u0 p0 c0 {4,S} {6,D} {14,S}
6 C u0 p0 c0 {5,D} {7,S} {15,S}
7 C u0 p0 c0 {6,S} {8,D} {16,S}
8 C u0 p0 c0 {7,D} {9,S} {17,S}
9 C u0 p0 c0 {4,S} {8,S} {10,D}
10 C u0 p0 c0 {1,S} {9,D} {18,S}
11 H u0 p0 c0 {1,S}
12 H u0 p0 c0 {2,S}
13 H u0 p0 c0 {3,S}
14 H u0 p0 c0 {5,S}
15 H u0 p0 c0 {6,S}
16 H u0 p0 c0 {7,S}
17 H u0 p0 c0 {8,S}
18 H u0 p0 c0 {10,S}
"""
fragment = afm.fragment.Fragment().fromAdjacencyList(adj)
frag_res = resonance.generate_resonance_structures(fragment,
clarStructures=True)
self.assertEqual(len(frag_res), 3)
def generate_resonance_structures(self,
keep_isomorphic=False,
filter_structures=True):
"""Returns a list of resonance structures of the fragment."""
return resonance.generate_resonance_structures(
self,
keep_isomorphic=keep_isomorphic,
filter_structures=filter_structures)
def penalty_for_o4tc_test(self):
"""Test that an O4tc atomtype with octet 8 gets penalized in the electronegativity heuristic"""
adj = """
1 S u0 p1 c0 {2,S} {3,T}
2 O u0 p3 c-1 {1,S}
3 O u0 p1 c+1 {1,T}
"""
mol = Molecule().from_adjacency_list(adj)
octet_deviation = get_octet_deviation(mol)
self.assertEqual(octet_deviation, 0)
self.assertEqual(mol.vertices[2].atomtype.label, 'O4tc')
mol_list = generate_resonance_structures(mol)
self.assertEqual(len(mol_list), 2)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
self.assertTrue(atom.charge == 0)
def penalty_for_O4tc_test(self):
"""Test that an O4tc atomType with octet 8 gets penalized in the electronegativity heuristic"""
adj = """
1 S u0 p1 c0 {2,S} {3,T}
2 O u0 p3 c-1 {1,S}
3 O u0 p1 c+1 {1,T}
"""
mol = Molecule().fromAdjacencyList(adj)
octet_deviation = get_octet_deviation(mol)
self.assertEqual(octet_deviation, 0)
self.assertEqual(mol.vertices[2].atomType.label, 'O4tc')
mol_list = generate_resonance_structures(mol)
self.assertEqual(len(mol_list), 2)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
self.assertTrue(atom.charge == 0)
def penalty_birads_replacing_lone_pairs_test(self):
"""Test that birads on `S u2 p0` are penalized"""
adj = """
multiplicity 3
1 S u2 p0 c0 {2,D} {3,D}
2 O u0 p2 c0 {1,D}
3 O u0 p2 c0 {1,D}
"""
mol = Molecule().fromAdjacencyList(adj)
mol.update()
mol_list = generate_resonance_structures(mol, keep_isomorphic=False, filter_structures=True)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
if atom.isSulfur():
self.assertNotEquals(atom.radicalElectrons, 2)
self.assertEqual(len(mol_list), 3)
self.assertEqual(sum([1 for mol in mol_list if mol.reactive]), 2)
def penalty_birads_replacing_lone_pairs_test(self):
"""Test that birads on `S u2 p0` are penalized"""
adj = """
multiplicity 3
1 S u2 p0 c0 {2,D} {3,D}
2 O u0 p2 c0 {1,D}
3 O u0 p2 c0 {1,D}
"""
mol = Molecule().from_adjacency_list(adj)
mol.update()
mol_list = generate_resonance_structures(mol, keep_isomorphic=False, filter_structures=True)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
if atom.is_sulfur():
self.assertNotEquals(atom.radical_electrons, 2)
self.assertEqual(len(mol_list), 3)
self.assertEqual(sum([1 for mol in mol_list if mol.reactive]), 2)