The flags are meant to be bit-wise combined BTW (see doc here: https://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/smiles/SmilesGenerator.html ):
I think you probably just want: SmilesGenerator generator1 = new SmilesGenerator(SmiFlavor.Absolute|SmiFlavor.AtomAtomMap); or SmilesGenerator generator1 = new SmilesGenerator(SmiFlavor.Canonical|SmiFlavor.AtomAtomMap);
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