def generateAromaticResonanceIsomers(mol):
"""
Generate the aromatic form of the molecule.
Returns it as a single element of a list.
If there's an error (eg. in RDKit) it just returns an empty list.
"""
cython.declare(molecule=Molecule, rdAtomIndices=dict, aromatic=cython.bint, aromaticBonds=list)
cython.declare(rings=list, ring0=list, i=cython.int, atom1=Atom, atom2=Atom, bond=Bond)
from rdkit.Chem.rdchem import BondType
AROMATIC = BondType.AROMATIC
# Radicals
if not mol.isCyclic():
return []
molecule = mol.copy(deep=True)
# In RMG, only 6-member rings can be considered aromatic, so ignore all other rings
rings = [ring0 for ring0 in molecule.getSmallestSetOfSmallestRings() if len(ring0) == 6]
if not rings:
return []
try:
rdkitmol, rdAtomIndices = generator.toRDKitMol(molecule, removeHs=False, returnMapping=True)
except ValueError:
return []
aromatic = False
for ring0 in rings:
aromaticBonds = []
# Figure out which atoms and bonds are aromatic and reassign appropriately:
for i, atom1 in enumerate(ring0):
if not atom1.isCarbon():
# all atoms in the ring must be carbon in RMG for our definition of aromatic
break
for atom2 in ring0[i + 1:]:
if molecule.hasBond(atom1, atom2):
if rdkitmol.GetBondBetweenAtoms(rdAtomIndices[atom1], rdAtomIndices[atom2]).GetBondType() is AROMATIC:
aromaticBonds.append(molecule.getBond(atom1, atom2))
else: # didn't break so all atoms are carbon
if len(aromaticBonds) == 6:
aromatic = True
# Only change bonds if there are all 6 are aromatic. Otherwise don't do anything
for bond in aromaticBonds:
bond.order = 'B'
if aromatic:
try:
molecule.updateAtomTypes(logSpecies=False)
except:
# Something incorrect has happened, ie. 2 double bonds on a Cb atomtype
# Do not add the new isomer since it is malformed
return []
else:
# nothing bad happened
return [molecule]
else:
return []
def generateAromaticResonanceIsomers(mol):
"""
Generate the aromatic form of the molecule.
"""
cython.declare(isomers=list, molecule=Molecule, rdAtomIndices=dict, aromatic=cython.bint, aromaticBonds=list)
cython.declare(rings=list, ring0=list, i=cython.int, atom1=Atom, atom2=Atom, bond=Bond)
isomers = []
# Radicals
if mol.isCyclic():
molecule = mol.copy(deep=True)
try:
rdkitmol, rdAtomIndices = generator.toRDKitMol(molecule, removeHs=False, returnMapping=True)
except:
return []
aromatic = False
rings = molecule.getSmallestSetOfSmallestRings()
for ring0 in rings:
# In RMG, only 6-member rings can be considered aromatic, so ignore all other rings
aromaticBonds = []
if len(ring0) == 6:
# Figure out which atoms and bonds are aromatic and reassign appropriately:
for i, atom1 in enumerate(ring0):
if not atom1.isCarbon():
# all atoms in the ring must be carbon in RMG for our definition of aromatic
break
for atom2 in ring0[i+1:]:
if molecule.hasBond(atom1, atom2):
if str(rdkitmol.GetBondBetweenAtoms(rdAtomIndices[atom1],rdAtomIndices[atom2]).GetBondType()) == 'AROMATIC':
aromaticBonds.append(molecule.getBond(atom1, atom2))
if len(aromaticBonds) == 6:
aromatic = True
# Only change bonds if there are all 6 are aromatic. Otherwise don't do anything
for bond in aromaticBonds:
bond.order = 'B'
if aromatic:
try:
molecule.updateAtomTypes()
isomers.append(molecule)
except:
# Something incorrect has happened, ie. 2 double bonds on a Cb atomtype
# Do not add the new isomer since it is malformed
pass
return isomers
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]
