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RearrangementLonePairReactionTest.java
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RearrangementLonePairReactionTest.java
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/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2007 Miguel Rojas <miguel.rojas@uni-koeln.de>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.reaction.type;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.LonePair;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionProcessTest;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;
/**
* <p>IReactionProcess which participate in movement resonance.
* This reaction could be represented as |A-B=C => [A+]=B-[C-]. Due to
* the negative charge of the atom A, the double bond in position 2 is
* displaced.</p>
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
* IReactionProcess type = new RearrangementLonePairReaction();
* HashMap<String,Object> params = new HashMap<String,Object>();
params.put("hasActiveCenter",Boolean.FALSE);;
type.setParameters(params);
* IReactionSet setOfReactions = type.initiate(setOfReactants, null);
* </pre>
*
* <p>We have the possibility to localize the reactive center. Good method if you
* want to localize the reaction in a fixed point</p>
* <pre>atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);</pre>
* <p>Moreover you must put the parameter Boolean.TRUE</p>
* <p>If the reactive center is not localized then the reaction process will
* try to find automatically the possible reactive center.</p>
*
*
* @author Miguel Rojas
*
* @cdk.created 2006-05-05
* @cdk.module test-reaction
* @cdk.set reaction-types
*
**/
/**
* TestSuite that runs a test for the RearrangementLonePairReactionTest.
* Generalized Reaction: [A-]-B=C => A=B-[C-].
*
* @cdk.module test-reaction
*/
public class RearrangementLonePairReactionTest extends ReactionProcessTest {
private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
/**
* The JUnit setup method
*/
public RearrangementLonePairReactionTest() throws Exception {
setReaction(RearrangementLonePairReaction.class);
}
/**
* The JUnit setup method
*/
@Test public void testRearrangementLonePairReaction() throws Exception {
IReactionProcess type = new RearrangementLonePairReaction();
Assert.assertNotNull(type);
}
/**
* A unit test suite for JUnit. Reaction: O-C=C-C => [O+]=C-[C-]-C
* Automatic search of the center active.
*
* @cdk.inchi InChI=1/C3H6O/c1-2-3-4/h2-4H,1H3
*
* @return The test suite
*/
@Test public void testInitiate_IMoleculeSet_IMoleculeSet() throws Exception {
IReactionProcess type = new RearrangementLonePairReaction();
IMoleculeSet setOfReactants = getExampleReactants();
IMolecule molecule = setOfReactants.getMolecule(0);
/* 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(1, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
Assert.assertEquals(-1, product.getAtom(2).getFormalCharge().intValue());
Assert.assertEquals(0, product.getConnectedLonePairsCount(molecule.getAtom(1)));
IMolecule molecule2 = getExpectedProducts().getMolecule(0);
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,queryAtom));
}
/**
* A unit test suite for JUnit. Reaction: O-C=C-C => [O+]=C-[C-]-C
* Manually put of the center active.
*
* @cdk.inchi InChI=1/C3H6O/c1-2-3-4/h2-4H,1H3
*
* @return The test suite
*/
@Test public void testManuallyCentreActive() throws Exception {
IReactionProcess type = new RearrangementLonePairReaction();
IMoleculeSet setOfReactants = getExampleReactants();
IMolecule molecule = setOfReactants.getMolecule(0);
/*manually put the center active*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getBond(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(3).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);
Assert.assertEquals(1, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
/*C=C-[C-]-C*/
IMolecule molecule2 = getExpectedProducts().getMolecule(0);
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(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 RearrangementLonePairReaction();
IMoleculeSet setOfReactants = getExampleReactants();
IMolecule molecule = setOfReactants.getMolecule(0);
/*manually put the reactive center*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getBond(1).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);
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.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test public void testMapping() throws Exception {
IReactionProcess type = new RearrangementLonePairReaction();
IMoleculeSet setOfReactants = getExampleReactants();
IMolecule molecule = setOfReactants.getMolecule(0);
molecule.addLonePair(new LonePair(molecule.getAtom(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);
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
Assert.assertEquals(5,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));
mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(2));
Assert.assertEquals(mappedProductA1, product.getAtom(2));
}
/**
* Test to recognize if this IMolecule_1 matches correctly into the CDKAtomTypes.
*/
@Test public void testAtomTypesMolecule1() throws Exception{
IMolecule moleculeTest = getExampleReactants().getMolecule(0);
makeSureAtomTypesAreRecognized(moleculeTest);
}
/**
* Test to recognize if this IMolecule_2 matches correctly into the CDKAtomTypes.
*/
@Test public void testAtomTypesMolecule2() throws Exception{
IMolecule moleculeTest = getExpectedProducts().getMolecule(0);
makeSureAtomTypesAreRecognized(moleculeTest);
}
/**
* get the molecule 1: O-C=C-C
*
* @cdk.inchi InChI=1/C3H6O/c1-2-3-4/h2-4H,1H3
*
* @return The IMoleculeSet
*/
private IMoleculeSet getExampleReactants() {
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("O"));
molecule.addLonePair(new LonePair(molecule.getAtom(0)));
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(1, 2, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
lpcheck.saturate(molecule);
} catch (Exception e) {
e.printStackTrace();
}
setOfReactants.addMolecule(molecule);
return setOfReactants;
}
/**
* Get the expected set of molecules.
*
* @return The IMoleculeSet
*/
private IMoleculeSet getExpectedProducts() {
IMoleculeSet setOfProducts = builder.newMoleculeSet();
//[O+]=C-[C-]-C
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("O"));
molecule.getAtom(0).setFormalCharge(+1);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("C"));
molecule.getAtom(2).setFormalCharge(-1);
molecule.addLonePair(new LonePair(molecule.getAtom(2)));
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
lpcheck.saturate(molecule);
} catch (Exception e) {
e.printStackTrace();
}
setOfProducts.addMolecule(molecule);
return setOfProducts;
}
/**
* Test to recognize if a IMolecule matcher correctly identifies the CDKAtomTypes.
*
* @param molecule The IMolecule to analyze
* @throws CDKException
*/
private void makeSureAtomTypesAreRecognized(IMolecule molecule) throws Exception {
Iterator<IAtom> atoms = molecule.atoms().iterator();
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
while (atoms.hasNext()) {
IAtom nextAtom = atoms.next();
Assert.assertNotNull(
"Missing atom type for: " + nextAtom,
matcher.findMatchingAtomType(molecule, nextAtom)
);
}
}
/**
* A unit test suite for JUnit: Resonance Fluorobenzene Fc1ccccc1 <=> ...
*
* InChI=1/C6H5F/c7-6-4-2-1-3-5-6/h1-5H
*
* @return The test suite
*/
@Test public void testFluorobenzene() throws Exception {
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("F"));
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(1, 2, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(3, 4, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(4, 5, IBond.Order.SINGLE);
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(5, 6, IBond.Order.DOUBLE);
molecule.addBond(6, 1, IBond.Order.SINGLE);
addExplicitHydrogens(molecule);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
lpcheck.saturate(molecule);
IReactionProcess type = new RearrangementLonePairReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
/*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);
Assert.assertEquals(1, setOfReactions.getReactionCount());
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
IMolecule molecule1 = builder.newMolecule();
molecule1.addAtom(builder.newAtom("F"));
molecule1.getAtom(0).setFormalCharge(1);
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(0, 1, IBond.Order.DOUBLE);
molecule1.addAtom(builder.newAtom("C"));
molecule1.getAtom(2).setFormalCharge(-1);
molecule1.addBond(1, 2, IBond.Order.SINGLE);
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(2, 3, IBond.Order.SINGLE);
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(3, 4, IBond.Order.DOUBLE);
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(4, 5, IBond.Order.SINGLE);
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(5, 6, IBond.Order.DOUBLE);
molecule1.addBond(6, 1, IBond.Order.SINGLE);
addExplicitHydrogens(molecule1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule1);
lpcheck.saturate(molecule1);
QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product1,qAC));
}
}