def test_double_bond(self):
adj = """multiplicity 2
1 O u1 p1 c+1 {2,D}
2 N u0 p2 c-1 {1,D}"""
mol = Molecule().from_adjacency_list(adj)
paths = find_adj_lone_pair_radical_delocalization_paths(mol.atoms[0])
self.assertTrue(paths)
def generate_adj_lone_pair_radical_resonance_structures(mol):
"""
Generate all of the resonance structures formed by lone electron pair - radical shifts between adjacent atoms.
These resonance transformations do not involve changing bond orders.
NO2 example: O=[:N]-[::O.] <=> O=[N.+]-[:::O-]
(where ':' denotes a lone pair, '.' denotes a radical, '-' not in [] denotes a single bond, '-'/'+' denote charge)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom)
cython.declare(v1=Vertex, v2=Vertex)
structures = []
if mol.is_radical(): # Iterate over radicals in structure
for atom in mol.vertices:
paths = pathfinder.find_adj_lone_pair_radical_delocalization_paths(atom)
for atom1, atom2 in paths:
# Adjust to (potentially) new resonance structure
atom1.decrement_radical()
atom1.increment_lone_pairs()
atom1.update_charge()
atom2.increment_radical()
atom2.decrement_lone_pairs()
atom2.update_charge()
# Make a copy of structure
structure = mol.copy(deep=True)
# Restore current structure
atom1.increment_radical()
atom1.decrement_lone_pairs()
atom1.update_charge()
atom2.decrement_radical()
atom2.increment_lone_pairs()
atom2.update_charge()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass # Don't append resonance structure if it creates an undefined atomtype
else:
structures.append(structure)
return structures
def test_hoso(self):
smiles = "[O]SO"
mol = Molecule().from_smiles(smiles)
paths = find_adj_lone_pair_radical_delocalization_paths(mol.atoms[0])
self.assertTrue(paths)
def test_no2b(self):
smiles = "[O-][N+]=O"
mol = Molecule().from_smiles(smiles)
paths = find_adj_lone_pair_radical_delocalization_paths(mol.atoms[1])
self.assertTrue(paths)