@Test
public void testSFBug999330() throws Exception {

    String file1 = "data/mdl/5SD.mol";
    String file2 = "data/mdl/ADN.mol";
    IAtomContainer mol1 = new AtomContainer();
    IAtomContainer mol2 = new AtomContainer();
    InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(file1);
    new MDLV2000Reader(ins1, Mode.STRICT).read(mol1);
    InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(file2);
    new MDLV2000Reader(ins2, Mode.STRICT).read(mol2);
    AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol2);
    mol2 = new AtomContainer((AtomContainer) permutor.next());
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
    CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol1.getBuilder());
    adder.addImplicitHydrogens(mol1);
    Aromaticity.cdkLegacy().apply(mol1);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
    adder = CDKHydrogenAdder.getInstance(mol2.getBuilder());
    adder.addImplicitHydrogens(mol2);
    Aromaticity.cdkLegacy().apply(mol2);
    List<IAtomContainer> list1 = CDKMCS.getOverlaps(mol1, mol2, true);
    List<IAtomContainer> list2 = CDKMCS.getOverlaps(mol2, mol1, true);
    Assert.assertEquals(1, list1.size());
    Assert.assertEquals(1, list2.size());
    Assert.assertEquals((list1.get(0)).getAtomCount(),
            (list2.get(0)).getAtomCount());
}