def calculateAtomSymmetryNumber(molecule, atom):
"""
Return the symmetry number centered at `atom` in the structure. The
`atom` of interest must not be in a cycle.
"""
symmetryNumber = 1
single = 0
double = 0
triple = 0
benzene = 0
numNeighbors = 0
for bond in atom.edges.values():
if bond.isSingle():
single += 1
elif bond.isDouble():
double += 1
elif bond.isTriple():
triple += 1
elif bond.isBenzene():
benzene += 1
numNeighbors += 1
# If atom has zero or one neighbors, the symmetry number is 1
if numNeighbors < 2:
return symmetryNumber
# Create temporary structures for each functional group attached to atom
molecule0 = molecule
molecule = molecule0.copy(True)
atom = molecule.vertices[molecule0.vertices.index(atom)]
molecule.removeAtom(atom)
groups = molecule.split()
# Determine equivalence of functional groups around atom
groupIsomorphism = dict([(group, dict()) for group in groups])
for group1 in groups:
for group2 in groups:
if group1 is not group2 and group2 not in groupIsomorphism[group1]:
groupIsomorphism[group1][group2] = group1.isIsomorphic(group2)
groupIsomorphism[group2][group1] = groupIsomorphism[group1][group2]
elif group1 is group2:
groupIsomorphism[group1][group1] = True
count = [sum([int(groupIsomorphism[group1][group2]) for group2 in groups]) for group1 in groups]
for i in range(count.count(2) / 2):
count.remove(2)
for i in range(count.count(3) / 3):
count.remove(3)
count.remove(3)
for i in range(count.count(4) / 4):
count.remove(4)
count.remove(4)
count.remove(4)
count.sort()
count.reverse()
if atom.radicalElectrons == 0:
if single == 4:
# Four single bonds
if count == [4]:
symmetryNumber *= 12
elif count == [3, 1]:
symmetryNumber *= 3
elif count == [2, 2]:
symmetryNumber *= 2
elif count == [2, 1, 1]:
symmetryNumber *= 1
elif count == [1, 1, 1, 1]:
symmetryNumber *= 1
elif single == 3:
# Three single bonds
if count == [3]:
symmetryNumber *= 3
elif count == [2, 1]:
symmetryNumber *= 1
elif count == [1, 1, 1]:
symmetryNumber *= 1
elif single == 2:
# Two single bonds
if count == [2]:
symmetryNumber *= 2
elif double == 2:
# Two double bonds
if count == [2]:
symmetryNumber *= 2
elif atom.radicalElectrons == 1:
if single == 3:
# Three single bonds
if count == [3]:
symmetryNumber *= 6
elif count == [2, 1]:
symmetryNumber *= 2
elif count == [1, 1, 1]:
symmetryNumber *= 1
elif atom.radicalElectrons == 2:
if single == 2:
# Two single bonds
if count == [2]:
symmetryNumber *= 2
if atom.isNitrogen():
for groupN in groups:
if groupN.toSMILES() == "[N+](=O)[O-]":
symmetryNumber *= 2
return symmetryNumber
def calculateAtomSymmetryNumber(molecule, atom):
"""
Return the symmetry number centered at `atom` in the structure. The
`atom` of interest must not be in a cycle.
"""
symmetryNumber = 1
single = 0
double = 0
triple = 0
benzene = 0
numNeighbors = 0
for bond in atom.edges.values():
if bond.isSingle(): single += 1
elif bond.isDouble(): double += 1
elif bond.isTriple(): triple += 1
elif bond.isBenzene(): benzene += 1
numNeighbors += 1
# If atom has zero or one neighbors, the symmetry number is 1
if numNeighbors < 2: return symmetryNumber
# Create temporary structures for each functional group attached to atom
molecule0 = molecule
molecule = molecule0.copy(True)
atom = molecule.vertices[molecule0.vertices.index(atom)]
molecule.removeAtom(atom)
groups = molecule.split()
# Determine equivalence of functional groups around atom
groupIsomorphism = dict([(group, dict()) for group in groups])
for group1 in groups:
for group2 in groups:
if group1 is not group2 and group2 not in groupIsomorphism[group1]:
groupIsomorphism[group1][group2] = group1.isIsomorphic(group2)
groupIsomorphism[group2][group1] = groupIsomorphism[group1][
group2]
elif group1 is group2:
groupIsomorphism[group1][group1] = True
count = [
sum([int(groupIsomorphism[group1][group2]) for group2 in groups])
for group1 in groups
]
for i in range(count.count(2) / 2):
count.remove(2)
for i in range(count.count(3) / 3):
count.remove(3)
count.remove(3)
for i in range(count.count(4) / 4):
count.remove(4)
count.remove(4)
count.remove(4)
count.sort()
count.reverse()
if atom.radicalElectrons == 0:
if single == 4:
# Four single bonds
if count == [4]: symmetryNumber *= 12
elif count == [3, 1]: symmetryNumber *= 3
elif count == [2, 2]: symmetryNumber *= 2
elif count == [2, 1, 1]: symmetryNumber *= 1
elif count == [1, 1, 1, 1]:
symmetryNumber *= 0.5 # found chirality
elif single == 3:
# Three single bonds
if count == [3]: symmetryNumber *= 3
elif count == [2, 1]: symmetryNumber *= 1
elif count == [1, 1, 1]: symmetryNumber *= 1
elif single == 2:
# Two single bonds
if count == [2]: symmetryNumber *= 2
# for resonance hybrids
elif single == 1:
if count == [2, 1]: symmetryNumber *= 2
elif double == 2:
# Two double bonds
if count == [2]: symmetryNumber *= 2
# for nitrogen resonance hybrids
elif single == 0:
if count == [2]: symmetryNumber *= 2
elif atom.radicalElectrons == 1:
if single == 3:
# Three single bonds
if count == [3]: symmetryNumber *= 6
elif count == [2, 1]: symmetryNumber *= 2
elif count == [1, 1, 1]: symmetryNumber *= 1
elif atom.radicalElectrons == 2:
if single == 2:
# Two single bonds
if count == [2]:
symmetryNumber *= 2
return symmetryNumber