def ToCannonicalSmiles(self):
atomCache={}
mol=OBMol()
for sourceAtom in self.atoms:
atom=mol.NewAtom()
atom.SetAtomicNum(sourceAtom.GetAtomicNum())
if sourceAtom.IsAromatic():
atom.SetAromatic()
atom.SetSpinMultiplicity(2)
atomCache[sourceAtom]=atom
for sourceBond in self.bonds:
mol.AddBond(atomCache[sourceBond.atom1].GetIdx(), atomCache[sourceBond.atom2].GetIdx(), sourceBond.GetBondOrder())
writer=OBConversion()
writer.SetInAndOutFormats("smi", "can")
return writer.WriteString(mol).strip()
def ToOBMol(self):
atomCache={}
mol=OBMol()
mol.BeginModify()
for sourceAtom in self.atoms:
atom=mol.NewAtom()
atom.SetAtomicNum(sourceAtom.GetAtomicNum())
if sourceAtom.IsAromatic():
atom.SetAromatic()
## atom.SetSpinMultiplicity(2)
atomCache[sourceAtom]=atom
for sourceBond in self.bonds:
mol.AddBond(atomCache[sourceBond.atom1].GetIdx(), atomCache[sourceBond.atom2].GetIdx(), sourceBond.GetBondOrder())
## mol.SetAromaticPerceived()
mol.AssignSpinMultiplicity()
## mol.UnsetAromaticPerceived()
mol.EndModify()
return mol