/**
* This method calculates the ionization potential of an atom.
*
* @param atom The IAtom to ionize.
* @param container Parameter is the IAtomContainer.
* @return The ionization potential. Not possible the ionization.
*/
@Override
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
double value = 0;
// FIXME: for now I'll cache a few modified atomic properties, and restore them at the end of
// this method
String originalAtomtypeName = atom.getAtomTypeName();
Integer originalNeighborCount = atom.getFormalNeighbourCount();
Integer originalValency = atom.getValency();
IAtomType.Hybridization originalHybrid = atom.getHybridization();
Double originalBondOrderSum = atom.getBondOrderSum();
Order originalMaxBondOrder = atom.getMaxBondOrder();
if (!isCachedAtomContainer(container)) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(container);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
getDescriptorNames(),
e);
}
}
try {
value = IonizationPotentialTool.predictIP(container, atom);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
getDescriptorNames(),
e);
}
// restore original props
atom.setAtomTypeName(originalAtomtypeName);
atom.setFormalNeighbourCount(originalNeighborCount);
atom.setValency(originalValency);
atom.setHybridization(originalHybrid);
atom.setMaxBondOrder(originalMaxBondOrder);
atom.setBondOrderSum(originalBondOrderSum);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(value),
getDescriptorNames());
}
/**
* A unit test for JUnit with C=CCCl # C=CC[Cl+*]
*
* @cdk.inchi InChI=1/C3H7Cl/c1-2-3-4/h2-3H2,1H3
*/
@Test
public void testCompareIonized() throws 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.assertNotSame(resultA, resultB);
}
/**
* 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());
}
/**
* Get the Ethene structure.
*
* @return The IMolecule
* @throws CDKException
*/
private IMolecule getEthene() throws Exception {
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addBond(0, 2, IBond.Order.SINGLE);
molecule.addBond(0, 3, IBond.Order.SINGLE);
molecule.addBond(1, 4, IBond.Order.SINGLE);
molecule.addBond(1, 5, IBond.Order.SINGLE);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(molecule);
return molecule;
}
@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);
}