def generateKekulizedResonanceIsomers(mol):
"""
Generate the kekulized (single-double bond) form of the molecule.
"""
cython.declare(isomers=list, atom=Atom)
isomers = []
for atom in mol.atoms:
if atom.atomType.label == 'Cb' or atom.atomType.label == 'Cbf':
break
else:
return isomers
rdkitmol = generator.toRDKitMol(mol) # This perceives aromaticit
isomer = parser.fromRDKitMol(Molecule(), rdkitmol)# This step Kekulizes the molecule
isomer.updateAtomTypes()
isomers.append(isomer)
return isomers
def generateKekulizedResonanceIsomers(mol):
"""
Generate a kekulized (single-double bond) form of the molecule.
Returns a single Kekule form, as an element of a list of length 1.
If there's an error (eg. in RDKit) then it just returns an empty list.
"""
cython.declare(atom=Atom)
for atom in mol.atoms:
if atom.atomType.label == "Cb" or atom.atomType.label == "Cbf":
break
else:
return []
try:
rdkitmol = generator.toRDKitMol(mol) # This perceives aromaticity
isomer = parser.fromRDKitMol(Molecule(), rdkitmol) # This step Kekulizes the molecule
except ValueError:
return []
isomer.updateAtomTypes()
return [isomer]
def generateKekulizedResonanceIsomers(mol):
"""
Generate a kekulized (single-double bond) form of the molecule.
Returns a single Kekule form, as an element of a list of length 1.
If there's an error (eg. in RDKit) then it just returns an empty list.
"""
cython.declare(atom=Atom)
for atom in mol.atoms:
if atom.atomType.label == 'Cb' or atom.atomType.label == 'Cbf':
break
else:
return []
try:
rdkitmol = generator.toRDKitMol(mol) # This perceives aromaticity
isomer = parser.fromRDKitMol(Molecule(), rdkitmol) # This step Kekulizes the molecule
except ValueError:
return []
isomer.updateAtomTypes(logSpecies=False)
return [isomer]
def generateKekuleStructure(mol):
"""
Generate a kekulized (single-double bond) form of the molecule.
The specific arrangement of double bonds is non-deterministic, and depends on RDKit.
Returns a single Kekule structure as an element of a list of length 1.
If there's an error (eg. in RDKit) then it just returns an empty list.
"""
cython.declare(atom=Atom)
for atom in mol.atoms:
if atom.atomType.label == 'Cb' or atom.atomType.label == 'Cbf':
break
else:
return []
try:
rdkitmol = generator.toRDKitMol(mol) # This perceives aromaticity
isomer = parser.fromRDKitMol(Molecule(), rdkitmol) # This step Kekulizes the molecule
except ValueError:
return []
isomer.updateAtomTypes(logSpecies=False)
return [isomer]