Hi,
another question, how can I add explict Hs and retain unfilled valences?
Example:
I have this:
C[N]C(=O)C(=O)C=O
and want this:
C([N](C(=O)C(=O)C(=O)[H]))([H])([H])[H]
but instead, I get this:
C(N(C(=O)C(=O)C(=O)[H])[H])([H])([H])[H]
My code:
String smiles = "C[N]C(=O)C(=O)C=O";
IAtomContainer mol = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHydrogenAdder adder =
CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance());
adder.addImplicitHydrogens(mol);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
System.out.println(SmilesGenerator.generic().create(mol));
Kind regards,
Martin
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