/**
* 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));
}
/**
* A unit test suite for JUnit.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMoleculeSet setOfReactants = builder.newMoleculeSet();
IMolecule molecule = getEthene();
/*manually putting the active center*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
setOfReactants.addMolecule(molecule);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IMolecule reactant = setOfReactions.getReaction(0).getReactants().getMolecule(0);
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
}
/**
* A unit test suite for JUnit. Reaction:
*
* @return The test suite
*/
@Test
@Override
public void testInitiate_IAtomContainerSet_IAtomContainerSet() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
/* 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(3, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
IAtomContainer molecule2 = getExpectedProducts().getAtomContainer(0);
IQueryAtomContainer queryAtom =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(new UniversalIsomorphismTester().isIsomorph(molecule2, queryAtom));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* manually put the reactive center */
molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER, true);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0);
Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
}
/**
* Get the resonance structures from an IMolecule.
*
* @param molecule The IMolecule to analyze
* @return The different resonance structures
*/
@TestMethod("testGetStructures_IMolecule")
public IMoleculeSet getStructures(IMolecule molecule) {
int countStructure = 0;
IMoleculeSet setOfMol = molecule.getBuilder().newMoleculeSet();
setOfMol.addMolecule(molecule);
for (int i = 0; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (IReactionProcess aReactionsList : reactionsList) {
IReactionProcess reaction = aReactionsList;
IMoleculeSet setOfReactants = molecule.getBuilder().newMoleculeSet();
setOfReactants.addMolecule(mol);
try {
IReactionSet setOfReactions = reaction.initiate(setOfReactants, null);
if (setOfReactions.getReactionCount() != 0)
for (int k = 0; k < setOfReactions.getReactionCount(); k++)
for (int j = 0;
j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount();
j++) {
IMolecule product = setOfReactions.getReaction(k).getProducts().getMolecule(j);
if (!existAC(setOfMol, product)) {
setOfMol.addMolecule(product);
countStructure++;
if (countStructure > maxStructures) return setOfMol;
}
}
} catch (CDKException e) {
e.printStackTrace();
}
}
}
return setOfMol;
}
private void callDefaultReactions() {
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
IReactionProcess type = new SharingLonePairReaction();
try {
type.setParameterList(paramList);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
type = new PiBondingMovementReaction();
List<IParameterReact> paramList2 = new ArrayList<IParameterReact>();
IParameterReact param2 = new SetReactionCenter();
param2.setParameter(Boolean.FALSE);
paramList2.add(param2);
try {
type.setParameterList(paramList2);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
type = new RearrangementAnionReaction();
try {
type.setParameterList(paramList);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
type = new RearrangementCationReaction();
try {
type.setParameterList(paramList);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
type = new RearrangementLonePairReaction();
try {
type.setParameterList(paramList);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
type = new RearrangementRadicalReaction();
try {
type.setParameterList(paramList);
} catch (CDKException e) {
e.printStackTrace();
}
reactionsList.add(type);
}
/**
* A unit test suite for JUnit.
*
* @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2
* @return The test suite
*/
@Test
public void testMapping() throws Exception {
IReactionProcess type = new AdductionProtonPBReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
IMolecule molecule = getEthene();
setOfReactants.addMolecule(molecule);
/*automatic looking for active center*/
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
Assert.assertEquals(3, setOfReactions.getReaction(0).getMappingCount());
IAtom mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(0));
Assert.assertEquals(mappedProductA1, product.getAtom(0));
mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(1));
Assert.assertEquals(mappedProductA1, product.getAtom(1));
IBond mappedProductB1 =
(IBond)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getBond(0));
Assert.assertEquals(mappedProductB1, product.getBond(0));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testMapping() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* automatic search of the center active */
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.FALSE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
Assert.assertEquals(19, setOfReactions.getReaction(0).getMappingCount());
IAtom mappedProductA1 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(0));
Assert.assertEquals(mappedProductA1, product.getAtom(0));
IAtom mappedProductA2 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(6));
Assert.assertEquals(mappedProductA2, product.getAtom(6));
IAtom mappedProductA3 =
(IAtom)
ReactionManipulator.getMappedChemObject(
setOfReactions.getReaction(0), molecule.getAtom(3));
Assert.assertEquals(mappedProductA3, product.getAtom(3));
}