/**
* A unit test suite for JUnit for Ethene. Reaction: O=C-C-H => O(H)-C=C. Automatic looking for
* active center.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testInitiate_IMoleculeSet_IMoleculeSet() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMolecule molecule = getEthene();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
/* initiate */
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
type.setParameterList(paramList);
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
Assert.assertEquals(2, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
IMolecule molecule2 = getExpected();
IQueryAtomContainer queryAtom =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2, queryAtom));
}
/**
* Checks if the given structures are isomorph.
*
* @param candidate1 the candidate1
* @param candidate2 the candidate2
* @return true, if is isomorph
* @throws CDKException the CDK exception
*/
public boolean isIsomorph(String candidate1, String candidate2) throws CDKException {
IAtomContainer cand1 = null;
IAtomContainer cand2 = null;
if (hasAtomContainer) {
cand1 = this.candidateToStructure.get(candidate1);
cand2 = this.candidateToStructure.get(candidate2);
} else {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
cand1 = sp.parseSmiles(candidatesToSmiles.get(candidate1));
cand2 = sp.parseSmiles(candidatesToSmiles.get(candidate2));
}
return UniversalIsomorphismTester.isIsomorph(cand1, cand2);
}
/**
* Search if the setOfAtomContainer contains the atomContainer
*
* @param set ISetOfAtomContainer object where to search
* @param atomContainer IAtomContainer to search
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
IAtomContainer acClone = null;
try {
acClone = (IMolecule) atomContainer.clone();
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
} catch (CloneNotSupportedException e1) {
e1.printStackTrace();
}
for (int i = 0; i < acClone.getAtomCount(); i++)
// if(acClone.getAtom(i).getID() == null)
acClone.getAtom(i).setID("" + acClone.getAtomNumber(acClone.getAtom(i)));
if (lookingSymmetry) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(acClone);
} catch (CDKException e) {
e.printStackTrace();
}
} else {
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int i = 0; i < set.getAtomContainerCount(); i++) {
IAtomContainer ss = set.getAtomContainer(i);
for (int j = 0; j < ss.getAtomCount(); j++)
// if(ss.getAtom(j).getID() == null)
ss.getAtom(j).setID("" + ss.getAtomNumber(ss.getAtom(j)));
try {
if (!lookingSymmetry) {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) {
QueryAtomContainer qAC2 =
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC2)) return true;
}
} else {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(acClone);
CDKHueckelAromaticityDetector.detectAromaticity(ss);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) return true;
}
} catch (CDKException e1) {
System.err.println(e1);
logger.error(e1.getMessage());
logger.debug(e1);
}
}
return false;
}