@Test
public void testSortResultsByStereoAndBondMatch() throws Exception {

    SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    IAtomContainer target = sp.parseSmiles("C\\C=C/OCC=C");
    IAtomContainer queryac = sp.parseSmiles("CCCOCC(C)=C");
    Isomorphism smsd = new Isomorphism(Algorithm.DEFAULT, false);
    smsd.init(queryac, target, true, true);
    smsd.setChemFilters(false, false, false);
    assertEquals(4, smsd.getAllAtomMapping().size());
    Isomorphism smsd1 = new Isomorphism(Algorithm.DEFAULT, false);
    smsd1.init(queryac, target, true, true);
    smsd1.setChemFilters(true, false, false);
    assertEquals(1, smsd1.getAllAtomMapping().size());
}