/**
* Applies the MDL valence model to atoms using the explicit valence (bond order sum) and charge
* to determine the correct number of implicit hydrogens. The model is not applied if the explicit
* valence is less than 0 - this is the case when a query bond was read for an atom.
*
* @param atom the atom to apply the model to
* @param explicitValence the explicit valence (bond order sum)
*/
private void applyMDLValenceModel(IAtom atom, int explicitValence) {
if (explicitValence < 0) return;
if (atom.getValency() != null) {
atom.setImplicitHydrogenCount(atom.getValency() - explicitValence);
} else {
Integer element = atom.getAtomicNumber();
if (element == null) return;
Integer charge = atom.getFormalCharge();
if (charge == null) charge = 0;
int implicitValence = MDLValence.implicitValence(element, charge, explicitValence);
atom.setValency(implicitValence);
atom.setImplicitHydrogenCount(implicitValence - explicitValence);
}
}
/**
* 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());
}