/** @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H */
@Test
public void xtestPyrrole() throws Exception {
IAtomContainer enol = new AtomContainer();
// atom block
IAtom atom1 = new Atom(Elements.CARBON);
atom1.setHybridization(Hybridization.SP2);
IAtom atom2 = new Atom(Elements.CARBON);
atom2.setHybridization(Hybridization.SP2);
IAtom atom3 = new Atom(Elements.CARBON);
atom3.setHybridization(Hybridization.SP2);
IAtom atom4 = new Atom(Elements.CARBON);
atom4.setHybridization(Hybridization.SP2);
IAtom atom5 = new Atom(Elements.NITROGEN);
atom5.setHybridization(Hybridization.SP2);
atom5.setImplicitHydrogenCount(1);
// bond block
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom2, atom3);
IBond bond3 = new Bond(atom3, atom4);
IBond bond4 = new Bond(atom4, atom5);
IBond bond5 = new Bond(atom5, atom1);
enol.addAtom(atom1);
enol.addAtom(atom2);
enol.addAtom(atom3);
enol.addAtom(atom4);
enol.addAtom(atom5);
enol.addBond(bond1);
enol.addBond(bond2);
enol.addBond(bond3);
enol.addBond(bond4);
enol.addBond(bond5);
// perceive atom types
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = fbot.kekuliseAromaticRings(enol);
Assert.assertNotNull(enol);
// Assert.assertTrue(fbot.isOK(enol));
// now check whether it did the right thing
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(0).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(1).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(2).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(3).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(4).getOrder());
;
}
/**
* 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());
}
/**
* Initiates the process for the given mechanism. The atoms to apply are mapped between reactants
* and products.
*
* @param atomContainerSet
* @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. The
* first atom is the atom which contains the ISingleElectron and the second third is the atom
* which will be removed the first atom
* @param bondList The list of bonds taking part in the mechanism. Only allowed one bond. It is
* the bond which is moved
* @return The Reaction mechanism
*/
@TestMethod(value = "testInitiate_IAtomContainerSet_ArrayList_ArrayList")
public IReaction initiate(
IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
throws CDKException {
CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(atomContainerSet.getBuilder());
if (atomContainerSet.getAtomContainerCount() != 1) {
throw new CDKException("RadicalSiteIonizationMechanism only expects one IMolecule");
}
if (atomList.size() != 3) {
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList");
}
if (bondList.size() != 2) {
throw new CDKException(
"RadicalSiteIonizationMechanism only expect one bond in the ArrayList");
}
IAtomContainer molecule = atomContainerSet.getAtomContainer(0);
IAtomContainer reactantCloned;
try {
reactantCloned = (IAtomContainer) molecule.clone();
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IMolecule!", e);
}
IAtom atom1 = atomList.get(0); // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
IAtom atom2 = atomList.get(1); // Atom
IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
IAtom atom3 = atomList.get(2); // Atom to be saved
IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
IBond bond1 = bondList.get(0); // Bond to increase the order
int posBond1 = molecule.getBondNumber(bond1);
IBond bond2 = bondList.get(1); // Bond to remove
int posBond2 = molecule.getBondNumber(bond2);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
reactantCloned.removeBond(reactantCloned.getBond(posBond2));
List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
reactantCloned.removeSingleElectron(selectron.get(selectron.size() - 1));
atom1C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
if (type == null) return null;
atom2C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
if (type == null) return null;
reactantCloned.addSingleElectron(new SingleElectron(atom3C));
atom3C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
if (type == null) return null;
IReaction reaction = DefaultChemObjectBuilder.getInstance().newInstance(IReaction.class);
reaction.addReactant(molecule);
/* mapping */
for (IAtom atom : molecule.atoms()) {
IMapping mapping =
DefaultChemObjectBuilder.getInstance()
.newInstance(
IMapping.class, atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
IAtomContainerSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.getAtomContainerCount(); z++)
reaction.addProduct((IAtomContainer) moleculeSetP.getAtomContainer(z));
return reaction;
}