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_for_s_triple_s_test(self):
"""Test that an S#S substructure in a molecule gets penalized in the octet deviation score"""
adj = """
1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
2 C u0 p0 c0 {4,S} {8,S} {9,S} {10,S}
3 S u0 p0 c0 {1,S} {4,T} {11,D}
4 S u0 p1 c0 {2,S} {3,T}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {2,S}
11 O u0 p2 c0 {3,D}
"""
mol = Molecule().from_adjacency_list(adj)
octet_deviation = get_octet_deviation(mol)
self.assertEqual(octet_deviation, 1.0)
def penalty_for_s_triple_s_test(self):
"""Test that an S#S substructure in a molecule gets penalized in the octet deviation score"""
adj = """
1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
2 C u0 p0 c0 {4,S} {8,S} {9,S} {10,S}
3 S u0 p0 c0 {1,S} {4,T} {11,D}
4 S u0 p1 c0 {2,S} {3,T}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {2,S}
11 O u0 p2 c0 {3,D}
"""
mol = Molecule().fromAdjacencyList(adj)
octet_deviation = get_octet_deviation(mol)
self.assertEqual(octet_deviation, 3.0)
def _generate_resonance_structures(mol_list, method_list, keep_isomorphic=False, copy=False, filter_structures=True):
"""
Iteratively generate all resonance structures for a list of starting molecules using the specified methods.
Args:
mol_list starting list of molecules
method_list list of resonance structure algorithms
keep_isomorphic if False, removes any structures that give is_isomorphic=True (default)
if True, only remove structures that give is_identical=True
copy if False, append new resonance structures to input list (default)
if True, make a new list with all of the resonance structures
"""
cython.declare(index=cython.int, molecule=Molecule, new_mol_list=list, new_mol=Molecule, mol=Molecule)
if copy:
# Make a copy of the list so we don't modify the input list
mol_list = mol_list[:]
min_octet_deviation = min(filtration.get_octet_deviation_list(mol_list))
min_charge_span = min(filtration.get_charge_span_list(mol_list))
# Iterate over resonance structures
index = 0
while index < len(mol_list):
molecule = mol_list[index]
new_mol_list = []
# On-the-fly filtration: Extend methods only for molecule that don't deviate too much from the octet rule
# (a +2 distance from the minimal deviation is used, octet deviations per species are in increments of 2)
# Sometimes rearranging the structure requires an additional higher charge span structure, so allow
# structures with a +1 higher charge span compared to the minimum, e.g., [O-]S#S[N+]#N
# This is run by default even if filter_structures=False.
octet_deviation = filtration.get_octet_deviation(molecule)
charge_span = molecule.get_charge_span()
if octet_deviation <= min_octet_deviation + 2 and charge_span <= min_charge_span + 1:
for method in method_list:
new_mol_list.extend(method(molecule))
if octet_deviation < min_octet_deviation:
# update min_octet_deviation to make this criterion tighter
min_octet_deviation = octet_deviation
if charge_span < min_charge_span:
# update min_charge_span to make this criterion tighter
min_charge_span = charge_span
for new_mol in new_mol_list:
# Append to structure list if unique
for mol in mol_list:
if not keep_isomorphic and mol.is_isomorphic(new_mol):
break
elif keep_isomorphic and mol.is_identical(new_mol):
break
else:
mol_list.append(new_mol)
# Move to the next resonance structure
index += 1
# check net charge
for mol in mol_list:
if mol.get_net_charge() != 0:
raise ResonanceError('Resonance generation gave a net charged molecule:\n{0}'
'Ions are not yet supported in RMG.'.format(
mol.to_adjacency_list()))
return mol_list