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[Cdk-commits] SF.net SVN: cdk: [10747] cdk/branches/miguelrojasch-charges/src
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From: <mig...@us...> - 2008-05-01 16:18:33
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Revision: 10747
http://cdk.svn.sourceforge.net/cdk/?rev=10747&view=rev
Author: miguelrojasch
Date: 2008-05-01 09:00:55 -0700 (Thu, 01 May 2008)
Log Message:
-----------
adjusted the hyperconjugationReaction to RearrangementChargeMechanishm
Modified Paths:
--------------
cdk/branches/miguelrojasch-charges/src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java
cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java
cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java
Modified: cdk/branches/miguelrojasch-charges/src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java
===================================================================
--- cdk/branches/miguelrojasch-charges/src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java 2008-05-01 15:00:15 UTC (rev 10746)
+++ cdk/branches/miguelrojasch-charges/src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java 2008-05-01 16:00:55 UTC (rev 10747)
@@ -25,27 +25,23 @@
package org.openscience.cdk.reaction.type;
+import java.util.ArrayList;
import java.util.Iterator;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionEngine;
import org.openscience.cdk.reaction.ReactionSpecification;
+import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism;
import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* <p>HyperconjugationReaction is the stabilizing interaction that results
@@ -83,7 +79,7 @@
**/
public class HyperconjugationReaction extends ReactionEngine implements IReactionProcess{
private LoggingTool logger;
- private CDKAtomTypeMatcher atMatcher;
+ private IReactionMechanism mechanism;
/**
* Constructor of the HyperconjugationReaction object
@@ -91,10 +87,7 @@
*/
public HyperconjugationReaction(){
logger = new LoggingTool(this);
- atMatcher = CDKAtomTypeMatcher.getInstance(
- NoNotificationChemObjectBuilder.getInstance(),
- CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
- );
+ mechanism = new RearrangementChargeMechanism();
}
/**
* Gets the specification attribute of the HyperconjugationReaction object
@@ -136,84 +129,50 @@
if(!(Boolean)paramsMap.get("hasActiveCenter")){
setActiveCenters(reactant);
}
- Iterator<IAtom> atoms = reactants.getMolecule(0).atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next();
- if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() == 1){
+ Iterator<IAtom> atomis = reactant.atoms();
+ while(atomis.hasNext()){
+ IAtom atomi = atomis.next();
+ if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)&& atomi.getFormalCharge() == 1 ){
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
-
- while (bondis.hasNext()) {
- IBond bondi = bondis.next();
-
+ while(bondis.hasNext()){
+ IBond bondi = bondis.next();
+
if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)&& bondi.getOrder() == IBond.Order.SINGLE){
IAtom atomj = bondi.getConnectedAtom(atomi);
- if(atomj.getFlag(CDKConstants.REACTIVE_CENTER) && atomj.getFormalCharge() == 0){
-
+ if(atomj.getFlag(CDKConstants.REACTIVE_CENTER)
+ && (atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
+ && reactant.getConnectedSingleElectronsCount(atomj) == 0){
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
- while (bondjs.hasNext()) {
- IBond bondj = bondjs.next();
-
- if(bondj.equals(bondi))
- continue;
-
- if(bondj.getFlag(CDKConstants.REACTIVE_CENTER) && bondj.getOrder() == IBond.Order.SINGLE){
+ while(bondjs.hasNext()){
+ IBond bondj = bondjs.next();
+
+ if(bondj.equals(bondi))
+ continue;
+
+ if(bondj.getFlag(CDKConstants.REACTIVE_CENTER) && bondj.getOrder() == IBond.Order.SINGLE){
+ IAtom atomk = bondj.getConnectedAtom(atomj);
+ if(atomk.getFlag(CDKConstants.REACTIVE_CENTER)&&
+ reactant.getConnectedSingleElectronsCount(atomk) == 0 &&
+ (atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge()) == 0 &&
+ atomk.getSymbol().equals("H")){
- IAtom atomk = bondj.getConnectedAtom(atomj);
- if(atomk.getFlag(CDKConstants.REACTIVE_CENTER) && atomk.getSymbol().equals("H")
- && atomk.getFormalCharge() == 0 ){
-
- IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
- reaction.addReactant(reactant);
-
- /* positions atoms and bonds */
- int atomiP = reactant.getAtomNumber(atomi);
- int atomjP = reactant.getAtomNumber(atomj);
- int atomkP = reactant.getAtomNumber(atomk);
- int bondiP = reactant.getBondNumber(bondi);
- int bondjP = reactant.getBondNumber(bondj);
-
- /* action */
- IAtomContainer reactantCloned;
- try {
- reactantCloned = (IMolecule)reactant.clone();
- } catch (CloneNotSupportedException e) {
- throw new CDKException("Could not clone IMolecule!", e);
- }
+ ArrayList<IAtom> atomList = new ArrayList<IAtom>();
+ atomList.add(atomi);
+ atomList.add(atomj);
+ atomList.add(atomk);
+ ArrayList<IBond> bondList = new ArrayList<IBond>();
+ bondList.add(bondi);
+ bondList.add(bondj);
- BondManipulator.increaseBondOrder(reactantCloned.getBond(bondiP));
-
- int charge = reactantCloned.getAtom(atomiP).getFormalCharge();
- reactantCloned.getAtom(atomiP).setFormalCharge(charge-1);
-
- charge = reactantCloned.getAtom(atomkP).getFormalCharge();
- reactantCloned.getAtom(atomkP).setFormalCharge(charge+1);
-
- reactantCloned.removeBond(reactantCloned.getBond(bondjP));
-
-// // check if resulting atom type is reasonable
-// IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(atomiP));
-// if (type == null)continue;
-// type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(atomkP));
-// if (type == null)continue;
-
- /* mapping */
- IMapping mapping = atomi.getBuilder().newMapping(atomi, reactantCloned.getAtom(atomiP));
- reaction.addMapping(mapping);
- mapping = atomi.getBuilder().newMapping(atomj, reactantCloned.getAtom(atomjP));
- reaction.addMapping(mapping);
- mapping = atomi.getBuilder().newMapping(atomk, reactantCloned.getAtom(atomkP));
- reaction.addMapping(mapping);
- mapping = atomi.getBuilder().newMapping(bondi, reactantCloned.getBond(bondiP));
- reaction.addMapping(mapping);
-
- IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
- for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){
- reaction.addProduct(moleculeSet.getMolecule(z));
- }
-
- setOfReactions.addReaction(reaction);
+ IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
+ moleculeSet.addMolecule(reactant);
+ IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
+ if(reaction == null)
+ continue;
+ else
+ setOfReactions.addReaction(reaction);
}
}
}
@@ -222,8 +181,6 @@
}
}
}
-
-
return setOfReactions;
@@ -241,45 +198,47 @@
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
- Iterator<IAtom> atoms = reactant.atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next();
- if(atomi.getFormalCharge() == 1){
+ Iterator<IAtom> atomis = reactant.atoms();
+ while(atomis.hasNext()){
+ IAtom atomi = atomis.next();
+ if(atomi.getFormalCharge() == 1 ){
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
-
- while (bondis.hasNext()) {
- IBond bondi = bondis.next();
-
+ while(bondis.hasNext()){
+ IBond bondi = bondis.next();
+
if(bondi.getOrder() == IBond.Order.SINGLE){
IAtom atomj = bondi.getConnectedAtom(atomi);
- if(atomj.getFormalCharge() == 0){
-
+ if((atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
+ && reactant.getConnectedSingleElectronsCount(atomj) == 0){
+
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
- while (bondjs.hasNext()) {
- IBond bondj = bondjs.next();
-
- if(bondj.equals(bondi))
- continue;
-
- if(bondj.getOrder() == IBond.Order.SINGLE){
+ while(bondjs.hasNext()){
+ IBond bondj = bondjs.next();
+
+ if(bondj.equals(bondi))
+ continue;
+
+ if(bondj.getOrder() == IBond.Order.SINGLE){
+ IAtom atomk = bondj.getConnectedAtom(atomj);
+ if(reactant.getConnectedSingleElectronsCount(atomk) == 0 &&
+ (atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge()) == 0 &&
+ atomk.getSymbol().equals("H")){
- IAtom atomk = bondj.getConnectedAtom(atomj);
- if(atomk.getSymbol().equals("H")){
- atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
- atomj.setFlag(CDKConstants.REACTIVE_CENTER,true);
- atomk.setFlag(CDKConstants.REACTIVE_CENTER,true);
- bondi.setFlag(CDKConstants.REACTIVE_CENTER,true);
- bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
+ atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
+ atomj.setFlag(CDKConstants.REACTIVE_CENTER,true);
+ atomk.setFlag(CDKConstants.REACTIVE_CENTER,true);
+ bondi.setFlag(CDKConstants.REACTIVE_CENTER,true);
+ bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
}
- }
+
+ }
}
}
-
}
}
}
}
}
-}
+}
\ No newline at end of file
Modified: cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java
===================================================================
--- cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java 2008-05-01 15:00:15 UTC (rev 10746)
+++ cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java 2008-05-01 16:00:55 UTC (rev 10747)
@@ -30,6 +30,7 @@
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
@@ -40,10 +41,12 @@
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.QueryAtomContainerCreator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.reaction.IReactionProcess;
-import org.openscience.cdk.reaction.type.HyperconjugationReaction;
import org.openscience.cdk.reaction.ReactionProcessTest;
+import org.openscience.cdk.tools.manipulator.ReactionManipulator;
/**
* TestSuite that runs a test for the HyperconjugationReactionTest.
@@ -73,7 +76,6 @@
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
/*[C+]CC*/
-// IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]CC");
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.getAtom(0).setFormalCharge(1);
@@ -83,15 +85,6 @@
molecule.addBond(1, 2, IBond.Order.SINGLE);
addExplicitHydrogens(molecule);
-// for(int i = 0; i < 7 ; i++)
-// molecule.addAtom(new Atom("H"));
-// molecule.addBond(0, 3, IBond.Order.SINGLE);
-// molecule.addBond(0, 4, IBond.Order.SINGLE);
-// molecule.addBond(1, 5, IBond.Order.SINGLE);
-// molecule.addBond(1, 6, IBond.Order.SINGLE);
-// molecule.addBond(2, 7, IBond.Order.SINGLE);
-// molecule.addBond(2, 8, IBond.Order.SINGLE);
-// molecule.addBond(2, 9, IBond.Order.SINGLE);
setOfReactants.addMolecule(molecule);
/*automatic search of the center active*/
@@ -109,7 +102,6 @@
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
/*C=CC*/
-// IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C=CC");
IMolecule molecule2 = builder.newMolecule();
molecule2.addAtom(builder.newAtom("C"));
molecule2.addAtom(builder.newAtom("C"));
@@ -122,7 +114,6 @@
product = setOfReactions.getReaction(0).getProducts().getMolecule(1);
/*[H+]*/
-// molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[H+]");
molecule2 = builder.newMolecule();
molecule2.addAtom(builder.newAtom("H"));
molecule2.getAtom(0).setFormalCharge(1);
@@ -148,4 +139,217 @@
}
}
+ /**
+ * A unit test suite for JUnit. Reaction: [C-][C+]-C => [C-]C=C + [H+]
+ * Manually put of the center active.
+ *
+ * @return The test suite
+ */
+ @Test public void testManuallyCentreActive() throws Exception {
+ IReactionProcess type = new HyperconjugationReaction();
+
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ IMolecule molecule = getMolecule1();
+ setOfReactants.addMolecule(molecule);
+
+ /*manually put the center active*/
+ molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+
+ HashMap<String,Object> params = new HashMap<String,Object>();
+ params.put("hasActiveCenter",Boolean.TRUE);;
+ type.setParameters(params);
+
+ /* initiate */
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ Assert.assertEquals(1, setOfReactions.getReactionCount());
+ Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());
+
+ IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+
+ IMolecule molecule2 = getMolecule2();
+
+ IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,queryAtom));
+
+ }
+ /**
+ * A unit test suite for JUnit.
+ *
+ * @return The test suite
+ */
+ @Test public void testCentreActive() throws Exception {
+ IReactionProcess type = new HyperconjugationReaction();
+
+ HashMap<String,Object> params = type.getParameters();
+ Assert.assertTrue(params.get("hasActiveCenter") instanceof Boolean);
+ Assert.assertFalse((Boolean)params.get("hasActiveCenter"));
+
+ params = new HashMap<String,Object>();
+ params.put("hasActiveCenter",Boolean.TRUE);
+ type.setParameters(params);
+ Assert.assertTrue((Boolean)params.get("hasActiveCenter"));
+ }
+
+ /**
+ * A unit test suite for JUnit. Reaction: [C-][C+]-C => [C-]C=C + [H+]
+ * Automatic search of the center active.
+ *
+ * @return The test suite
+ */
+ @Test public void testWithNegativeCharge() throws Exception {
+ IReactionProcess type = new HyperconjugationReaction();
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+
+ IMolecule molecule = getMolecule1();
+ setOfReactants.addMolecule(molecule);
+
+ /*automatic search of the center active*/
+ HashMap<String,Object> params = new HashMap<String,Object>();
+ params.put("hasActiveCenter",Boolean.FALSE);;
+ type.setParameters(params);
+
+ /* initiate */
+ makeSureAtomTypesAreRecognized(molecule);
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ Assert.assertEquals(3, setOfReactions.getReactionCount());
+ Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());
+
+ IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+
+ IMolecule molecule2 = getMolecule2();
+
+ IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product,queryAtom));
+
+ product = setOfReactions.getReaction(0).getProducts().getMolecule(1);
+
+ molecule2 = builder.newMolecule();
+ molecule2.addAtom(builder.newAtom("H"));
+ molecule2.getAtom(0).setFormalCharge(1);
+
+ 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 HyperconjugationReaction();
+ IMoleculeSet setOfReactants = builder.newMoleculeSet();
+
+ IMolecule molecule = getMolecule1();
+
+ /*manually put the reactive center*/
+ molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+ setOfReactants.addMolecule(molecule);
+ HashMap<String,Object> params = new HashMap<String,Object>();
+ params.put("hasActiveCenter",Boolean.TRUE);;
+ type.setParameters(params);
+
+ /* initiate */
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ IMolecule reactant1 = setOfReactions.getReaction(0).getReactants().getMolecule(0);
+
+ Assert.assertTrue(molecule.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant1.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant1.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant1.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant1.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant1.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
+ }
+ /**
+ * A unit test suite for JUnit.
+ *
+ * @return The test suite
+ */
+ @Test public void testMapping() throws Exception {
+ IReactionProcess type = new HyperconjugationReaction();
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+
+ IMolecule molecule = getMolecule1();
+ setOfReactants.addMolecule(molecule);
+
+ /*automatic search of the center active*/
+ HashMap<String,Object> params = new HashMap<String,Object>();
+ params.put("hasActiveCenter",Boolean.FALSE);;
+ type.setParameters(params);
+
+ /* initiate */
+ makeSureAtomTypesAreRecognized(molecule);
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+ IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
+
+ Assert.assertEquals(3, setOfReactions.getReactionCount());
+ Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());
+
+ IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(1));
+ Assert.assertEquals(mappedProductA1, product1.getAtom(1));
+ IBond mappedProductB1 = (IBond)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getBond(1));
+ Assert.assertEquals(mappedProductB1, product1.getBond(3));
+ mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(2));
+ Assert.assertEquals(mappedProductA1, product1.getAtom(4));
+ mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(6));
+ Assert.assertEquals(mappedProductA1, product2.getAtom(0));
+ }
+ /**
+ * get the molecule 1: [C-]-[C+] - C
+ *
+ * @return The IMolecule
+ */
+ private IMolecule getMolecule1()throws Exception {
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.getAtom(0).setFormalCharge(-1);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.getAtom(1).setFormalCharge(+1);
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(1, 2, IBond.Order.SINGLE);
+ addExplicitHydrogens(molecule);
+
+ return molecule;
+ }
+ /**
+ * get the molecule 2: [C-]-C = C
+ *
+ * @return The IMolecule
+ */
+ private IMolecule getMolecule2()throws Exception {
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.getAtom(0).setFormalCharge(-1);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(1, 2, IBond.Order.DOUBLE);
+ addExplicitHydrogens(molecule);
+
+ return molecule;
+ }
+
}
Modified: cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java
===================================================================
--- cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java 2008-05-01 15:00:15 UTC (rev 10746)
+++ cdk/branches/miguelrojasch-charges/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java 2008-05-01 16:00:55 UTC (rev 10747)
@@ -52,8 +52,6 @@
* TestSuite that runs a test for the PiBondingMovemetReactionTest.
* Generalized Reaction: C1=C(C)-C(C)=C-C=C1 -> C1(C)=C(C)-C=C-C=C1.
*
- * FIXME: REACT: The tests fail if I don't put the smiles, strange
- *
* @cdk.module test-reaction
*/
public class PiBondingMovemetReactionTest extends ReactionProcessTest {
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