@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
// removeHydrogens does a deep copy, so no need to clone
IAtomContainer localAtomContainer = AtomContainerManipulator.removeHydrogens(container);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
Iterator<IAtom> atoms = localAtomContainer.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = atoms.next();
IAtomType type;
try {
type = matcher.findMatchingAtomType(localAtomContainer, atom);
AtomTypeManipulator.configure(atom, type);
} catch (Exception e) {
return getDummyDescriptorValue(new CDKException("Error in atom typing: " + e.getMessage()));
}
}
CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder());
try {
hAdder.addImplicitHydrogens(localAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(
new CDKException("Error in hydrogen addition: " + e.getMessage()));
}
List subgraph3 = order3(localAtomContainer);
List subgraph4 = order4(localAtomContainer);
List subgraph5 = order5(localAtomContainer);
List subgraph6 = order6(localAtomContainer);
double order3s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph3);
double order4s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph4);
double order5s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph5);
double order6s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph6);
double order3v, order4v, order5v, order6v;
try {
order3v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph3);
order4v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph4);
order5v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph5);
order6v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph6);
} catch (CDKException e) {
return getDummyDescriptorValue(
new CDKException("Error in substructure search: " + e.getMessage()));
}
DoubleArrayResult retval = new DoubleArrayResult();
retval.add(order3s);
retval.add(order4s);
retval.add(order5s);
retval.add(order6s);
retval.add(order3v);
retval.add(order4v);
retval.add(order5v);
retval.add(order6v);
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), retval, getDescriptorNames());
}
private List order6(IAtomContainer atomContainer) {
QueryAtomContainer[] queries = new QueryAtomContainer[5];
try {
queries[0] =
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(
sp.parseSmiles("CC(C)(C)CCC"), false);
queries[1] =
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(
sp.parseSmiles("CC(C)C(C)CC"), false);
queries[2] =
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(
sp.parseSmiles("CC(C)CC(C)C"), false);
queries[3] =
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(
sp.parseSmiles("CC(C)CCCC"), false);
queries[4] =
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(
sp.parseSmiles("CCC(C)CCC"), false);
} catch (InvalidSmilesException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
return ChiIndexUtils.getFragments(atomContainer, queries);
}