def generateN5dd_N5tsResonanceIsomers(mol):
"""
Generate all of the resonance isomers formed by shifts between N5dd and N5ts.
"""
cython.declare(isomers=list, paths=list, index=cython.int, isomer=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, atom3=Atom)
cython.declare(bond12=Bond, bond13=Bond)
cython.declare(v1=Vertex, v2=Vertex)
isomers = []
# Iterate over nitrogen atoms in structure
for atom in mol.vertices:
paths = pathfinder.findAllDelocalizationPathsN5dd_N5ts(atom)
for atom1, atom2, atom3, bond12, bond13, direction in paths:
# from N5dd to N5ts
if direction == 1:
# Adjust to (potentially) new resonance isomer
bond12.decrementOrder()
bond13.incrementOrder()
atom2.incrementLonePairs()
atom3.decrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# 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.connectivity = v1.connectivity
v2.sortingLabel = v1.sortingLabel
# Restore current isomer
bond12.incrementOrder()
bond13.decrementOrder()
atom2.decrementLonePairs()
atom3.incrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# Append to isomer list if unique
isomer.updateAtomTypes()
isomers.append(isomer)
# from N5ts to N5dd
if direction == 2:
# Adjust to (potentially) new resonance isomer
bond12.decrementOrder()
bond13.incrementOrder()
atom2.incrementLonePairs()
atom3.decrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# 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.connectivity = v1.connectivity
v2.sortingLabel = v1.sortingLabel
# Restore current isomer
bond12.incrementOrder()
bond13.decrementOrder()
atom2.decrementLonePairs()
atom3.incrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# Append to isomer list if unique
isomer.updateAtomTypes()
isomers.append(isomer)
return isomers
def generateN5dd_N5tsResonanceStructures(mol):
"""
Generate all of the resonance structures formed by shifts between N5dd and N5ts.
"""
cython.declare(isomers=list, paths=list, index=cython.int, isomer=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, atom3=Atom)
cython.declare(bond12=Bond, bond13=Bond)
cython.declare(v1=Vertex, v2=Vertex)
isomers = []
# Iterate over nitrogen atoms in structure
for atom in mol.vertices:
paths = pathfinder.findAllDelocalizationPathsN5dd_N5ts(atom)
for atom1, atom2, atom3, bond12, bond13, direction in paths:
# from N5dd to N5ts
if direction == 1:
# Adjust to (potentially) new resonance isomer
bond12.decrementOrder()
bond13.incrementOrder()
atom2.incrementLonePairs()
atom3.decrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# 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
bond12.incrementOrder()
bond13.decrementOrder()
atom2.decrementLonePairs()
atom3.incrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# Append to isomer list if unique
isomer.updateAtomTypes(logSpecies=False)
isomers.append(isomer)
# from N5ts to N5dd
if direction == 2:
# Adjust to (potentially) new resonance isomer
bond12.decrementOrder()
bond13.incrementOrder()
atom2.incrementLonePairs()
atom3.decrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# 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
bond12.incrementOrder()
bond13.decrementOrder()
atom2.decrementLonePairs()
atom3.incrementLonePairs()
atom1.updateCharge()
atom2.updateCharge()
atom3.updateCharge()
# Append to isomer list if unique
isomer.updateAtomTypes(logSpecies=False)
isomers.append(isomer)
return isomers