@Test public void testUseStereoElements() throws CDKException {

    final String smiles1  = "CC[C@@H](C)O";
    final String smiles2  = "CC[C@H](O)C";
    final String molfile = "\n"
                         + "  CDK     10121722462D          \n"
                         + "\n"
                         + "  5  4  0  0  0  0            999 V2000\n"
                         + "   -4.1837    2.6984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                         + "   -3.4692    3.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                         + "   -2.7547    2.6984    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n"
                         + "   -2.0403    3.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                         + "   -2.7547    1.8734    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
                         + "  1  2  1  0  0  0  0\n"
                         + "  2  3  1  0  0  0  0\n"
                         + "  3  4  1  0  0  0  0\n"
                         + "  3  5  1  1  0  0  0\n"
                         + "M  END\n";
    IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
    MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(molfile));
    SmilesParser smipar = new SmilesParser(bldr);
    IAtomContainer mol1 = smipar.parseSmiles(smiles1);
    IAtomContainer mol2 = smipar.parseSmiles(smiles2);
    IAtomContainer mol3 = mdlr.read(bldr.newAtomContainer());
    CircularFingerprinter fpr = new CircularFingerprinter();
    // when stereo-chemistry is perceived we don't have coordinates from the
    // SMILES and so get a different fingerprint
    fpr.setPerceiveStereo(true);
    org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol1), is(fpr.getFingerprint(mol2)));
    org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol2), is(not(fpr.getFingerprint(mol3))));
    fpr.setPerceiveStereo(false);
    org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol1), is(fpr.getFingerprint(mol2)));
    org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol2), is(fpr.getFingerprint(mol3)));
}