def generate_allyl_delocalization_resonance_structures(mol):
"""
Generate all of the resonance structures formed by one allyl radical shift.
Biradicals on a single atom are not supported.
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, atom3=Atom, bond12=Bond, bond23=Bond)
cython.declare(v1=Vertex, v2=Vertex)
structures = []
if mol.is_radical(): # Iterate over radicals in structure
for atom in mol.vertices:
paths = pathfinder.find_allyl_delocalization_paths(atom)
for atom1, atom2, atom3, bond12, bond23 in paths:
# Adjust to (potentially) new resonance structure
atom1.decrement_radical()
atom3.increment_radical()
bond12.increment_order()
bond23.decrement_order()
# Make a copy of structure
structure = mol.copy(deep=True)
# Restore current structure
atom1.increment_radical()
atom3.decrement_radical()
bond12.decrement_order()
bond23.increment_order()
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_nitrogenated_birad(self):
smiles = '[CH]=C[N]'
mol = Molecule().from_smiles(smiles)
paths = find_allyl_delocalization_paths(mol.atoms[3])
self.assertTrue(paths)
def test_allyl_radical(self):
smiles = "[CH2]C=C"
mol = Molecule().from_smiles(smiles)
paths = find_allyl_delocalization_paths(mol.atoms[0])
self.assertTrue(paths)
