gistfile1.java

// 水素原子の削除
molecule = (IMolecule) AtomContainerManipulator.removeHydrogens((IAtomContainer) molecule);
// 末端、ヘテロ原子上の水素のみ表示
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
for (IAtom atom : molecule.atoms()) {
    try {
        IAtomType type = matcher.findMatchingAtomType(molecule, atom);
        atom.setImplicitHydrogenCount(
                type.getFormalNeighbourCount() - molecule.getConnectedAtomsCount(atom));
    } catch (CDKException e) {
        e.printStackTrace();
    }
}