/**
* A unit test for JUnit
*
* @throws Exception
*/
@Test
public void testStabilizationComparative() throws Exception {
IAtomContainer mol1 = builder.newInstance(IAtomContainer.class);
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.getAtom(1).setFormalCharge(1);
mol1.addBond(0, 1, Order.SINGLE);
mol1.addAtom(builder.newInstance(IAtom.class, "C"));
mol1.addBond(1, 2, Order.SINGLE);
mol1.addAtom(builder.newInstance(IAtom.class, "O"));
mol1.addBond(1, 3, Order.SINGLE);
addExplicitHydrogens(mol1);
lpcheck.saturate(mol1);
DoubleResult result1 = ((DoubleResult) descriptor.calculate(mol1.getAtom(1), mol1).getValue());
IAtomContainer mol2 = builder.newInstance(IAtomContainer.class);
mol2.addAtom(builder.newInstance(IAtom.class, "C"));
mol2.addAtom(builder.newInstance(IAtom.class, "C"));
mol2.getAtom(1).setFormalCharge(1);
mol2.addBond(0, 1, Order.SINGLE);
mol2.addAtom(builder.newInstance(IAtom.class, "O"));
mol2.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol2);
lpcheck.saturate(mol2);
DoubleResult result2 = ((DoubleResult) descriptor.calculate(mol2.getAtom(1), mol2).getValue());
IAtomContainer mol3 = builder.newInstance(IAtomContainer.class);
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.getAtom(1).setFormalCharge(1);
mol3.addBond(0, 1, Order.SINGLE);
mol3.addAtom(builder.newInstance(IAtom.class, "C"));
mol3.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol3);
lpcheck.saturate(mol3);
DoubleResult result3 = ((DoubleResult) descriptor.calculate(mol3.getAtom(1), mol3).getValue());
Assert.assertTrue(result3.doubleValue() < result2.doubleValue());
Assert.assertTrue(result2.doubleValue() < result1.doubleValue());
}
@Test
public void testNotCharged() throws Exception {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(0).setFormalCharge(-1);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.addBond(0, 1, Order.DOUBLE);
mol.addAtom(builder.newInstance(IAtom.class, "F"));
mol.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol);
lpcheck.saturate(mol);
DoubleResult result = ((DoubleResult) descriptor.calculate(mol.getAtom(0), mol).getValue());
Assert.assertEquals(0.0, result.doubleValue(), 0.00001);
}