Simple, don't change the molecule :-). You only need atom types here to add hydrogens and you don't need to add hydrogens they're there already when read from SMILES.
String smiles = "C[N]C(=O)C(=O)C=O"; IAtomContainer mol = new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles); AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); System.out.println(SmilesGenerator.generic().create(mol));
------------------------------------------------------------------------------
_______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user