def generateAdjacentResonanceStructures(mol):
"""
Generate all of the resonance structures formed by one allyl radical shift.
Biradicals on a single atom are not supported.
"""
cython.declare(isomers=list, paths=list, index=cython.int, isomer=Molecule)
cython.declare(atom=Atom,
atom1=Atom,
atom2=Atom,
atom3=Atom,
bond12=Bond,
bond23=Bond)
cython.declare(v1=Vertex, v2=Vertex)
isomers = []
# Radicals
if mol.isRadical():
# Iterate over radicals in structure
for atom in mol.vertices:
paths = pathfinder.findAllDelocalizationPaths(atom)
for atom1, atom2, atom3, bond12, bond23 in paths:
# Adjust to (potentially) new resonance isomer
atom1.decrementRadical()
atom3.incrementRadical()
bond12.incrementOrder()
bond23.decrementOrder()
# Make a copy of isomer
isomer = mol.copy(deep=True)
# Also copy the connectivity values, since they are the same
# for all resonance forms
for index in range(len(mol.vertices)):
v1 = mol.vertices[index]
v2 = isomer.vertices[index]
v2.connectivity1 = v1.connectivity1
v2.connectivity2 = v1.connectivity2
v2.connectivity3 = v1.connectivity3
v2.sortingLabel = v1.sortingLabel
# Restore current isomer
atom1.incrementRadical()
atom3.decrementRadical()
bond12.decrementOrder()
bond23.incrementOrder()
# Append to isomer list if unique
isomer.updateAtomTypes(logSpecies=False)
isomers.append(isomer)
return isomers
def generateAdjacentResonanceStructures(mol):
"""
Generate all of the resonance structures formed by one allyl radical shift.
Biradicals on a single atom are not supported.
"""
cython.declare(isomers=list, paths=list, index=cython.int, isomer=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, atom3=Atom, bond12=Bond, bond23=Bond)
cython.declare(v1=Vertex, v2=Vertex)
isomers = []
# Radicals
if mol.isRadical():
# Iterate over radicals in structure
for atom in mol.vertices:
paths = pathfinder.findAllDelocalizationPaths(atom)
for atom1, atom2, atom3, bond12, bond23 in paths:
# Adjust to (potentially) new resonance isomer
atom1.decrementRadical()
atom3.incrementRadical()
bond12.incrementOrder()
bond23.decrementOrder()
# Make a copy of isomer
isomer = mol.copy(deep=True)
# Also copy the connectivity values, since they are the same
# for all resonance forms
for index in range(len(mol.vertices)):
v1 = mol.vertices[index]
v2 = isomer.vertices[index]
v2.connectivity1 = v1.connectivity1
v2.connectivity2 = v1.connectivity2
v2.connectivity3 = v1.connectivity3
v2.sortingLabel = v1.sortingLabel
# Restore current isomer
atom1.incrementRadical()
atom3.decrementRadical()
bond12.decrementOrder()
bond23.incrementOrder()
# Append to isomer list if unique
isomer.updateAtomTypes(logSpecies=False)
isomers.append(isomer)
return isomers