@Test
public void testCompareIonized() throws ClassNotFoundException, CDKException, java.lang.Exception {

    IAtomContainer molA = builder.newInstance(IAtomContainer.class);
    molA.addAtom(builder.newInstance(IAtom.class, "C"));
    molA.addAtom(builder.newInstance(IAtom.class, "C"));
    molA.addBond(0, 1, IBond.Order.SINGLE);
    molA.addAtom(builder.newInstance(IAtom.class, "C"));
    molA.addBond(1, 2, IBond.Order.SINGLE);
    molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
    molA.addBond(2, 3, IBond.Order.SINGLE);
    addExplicitHydrogens(molA);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
    lpcheck.saturate(molA);
    double resultA = ((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
    IAtomContainer molB = builder.newInstance(IAtomContainer.class);
    molB.addAtom(builder.newInstance(IAtom.class, "C"));
    molB.addAtom(builder.newInstance(IAtom.class, "C"));
    molB.addBond(0, 1, IBond.Order.SINGLE);
    molB.addAtom(builder.newInstance(IAtom.class, "C"));
    molB.addBond(1, 2, IBond.Order.SINGLE);
    molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
    molB.getAtom(3).setFormalCharge(1);
    molB.addSingleElectron(3);
    molB.addLonePair(3);
    molB.addLonePair(3);
    molB.addBond(2, 3, IBond.Order.SINGLE);
    addExplicitHydrogens(molB);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
    lpcheck.saturate(molB);
    Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
    Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
    Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
    double resultB = ((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
    Assert.assertEquals(resultA, resultB, 0.00001);
}