chempyformatics

UniqueSMILES.py

See also: the Groovy version

Source code

from scyjava import config, jimport
config.add_endpoints('org.openscience.cdk:cdk-bundle:2.9')
MoleculeFactory = jimport('org.openscience.cdk.templates.MoleculeFactory')
AtomContainerManipulator = jimport('org.openscience.cdk.tools.manipulator.AtomContainerManipulator')
CDKHueckelAromaticityDetector = jimport('org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector')
CDKHydrogenAdder = jimport('org.openscience.cdk.tools.CDKHydrogenAdder')
SmilesGenerator = jimport('org.openscience.cdk.smiles.SmilesGenerator')

mol = MoleculeFactory.makePhenylAmine()
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
hAdder = CDKHydrogenAdder.getInstance(mol.getBuilder())
hAdder.addImplicitHydrogens(mol)
generator = SmilesGenerator.unique()
smiles = generator.createSMILES(mol)
print(f"{smiles}")

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Output

NC=1C=CC=CC1