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[Cdk-commits] SF.net SVN: cdk: [10080] branches/miguelrojasch/reaction/src/org/ openscience/cdk
|
From: <mig...@us...> - 2008-02-12 23:45:15
|
Revision: 10080
http://cdk.svn.sourceforge.net/cdk/?rev=10080&view=rev
Author: miguelrojasch
Date: 2008-02-12 15:44:06 -0800 (Tue, 12 Feb 2008)
Log Message:
-----------
new Mechanism: RadicalIonizationMechanism. Emerged the reaction RadicalSite*Reaction into
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationHReactionTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationReactionTest.java
Added Paths:
-----------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java
Added: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java 2008-02-12 23:44:06 UTC (rev 10080)
@@ -0,0 +1,148 @@
+/* $Revision: 8418 $ $Author: egonw $ $Date: 2007-06-25 22:05:44 +0200 (Mon, 25 Jun 2007) $
+ *
+ * Copyright (C) 2008 Miguel Rojas <mig...@ya...>
+ *
+ * Contact: cdk...@li...
+ *
+ * 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.mechanism;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.SingleElectron;
+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.IAtomType;
+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.ISingleElectron;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.reaction.IReactionMechanism;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.BondManipulator;
+
+/**
+ * <p>This mechanism extracts an atom because of the stabilization of a radical.
+ * It returns the reaction mechanism which has been cloned the IMolecule.</p>
+ * <p>This reaction could be represented as Y-B-[C*] => [Y*] + B=C</p>
+ *
+ * @author miguelrojasch
+ * @cdk.created 2008-02-10
+ * @cdk.module reaction
+ *
+ */
+public class RadicalSiteIonizationMechanism implements IReactionMechanism{
+
+ private CDKAtomTypeMatcher atMatcher;
+
+ /**
+ * Constructor of the RadicalSiteIonizationMechanism object.
+ *
+ */
+ public RadicalSiteIonizationMechanism(){
+ atMatcher = CDKAtomTypeMatcher.getInstance(
+ NoNotificationChemObjectBuilder.getInstance(),
+ CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
+ );
+ }
+
+ /**
+ * Initiates the process for the given mechanism. The atoms to apply are mapped between
+ * reactants and products.
+ *
+ * @param molecule The IMolecule to apply the mechanism
+ * @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
+ *
+ */
+ public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
+ 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");
+ }
+ IMolecule reactantCloned;
+ try {
+ reactantCloned = (IMolecule) molecule.clone();
+ } catch (CloneNotSupportedException e) {
+ throw new CDKException("Could not clone IMolecule!", e);
+ }
+ IAtom atom1 = atomList.get(0);// Atom containing the ISingleElectron
+ int posAtom1 = molecule.getAtomNumber(atom1);
+ IAtom atom2 = atomList.get(1);// Atom
+ int posAtom2 = molecule.getAtomNumber(atom2);
+ IAtom atom3 = atomList.get(2);// Atom to be saved
+ int posAtom3 = 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(reactantCloned.getAtom(posAtom1));
+ reactantCloned.removeSingleElectron(selectron.get(selectron.size() -1));
+ reactantCloned.getAtom(posAtom1).setHybridization(null);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
+ IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom1));
+ if (type == null) return null;
+
+ reactantCloned.getAtom(posAtom2).setHybridization(null);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
+ type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom2));
+ if (type == null) return null;
+
+ reactantCloned.addSingleElectron(new SingleElectron(reactantCloned.getAtom(posAtom3)));
+ reactantCloned.getAtom(posAtom3).setHybridization(null);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
+ type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom3));
+ if (type == null) return null;
+
+ IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
+ reaction.addReactant(molecule);
+
+ /* mapping */
+ IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom1, reactantCloned.getAtom(posAtom1));
+ reaction.addMapping(mapping);
+ mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom2, reactantCloned.getAtom(posAtom2));
+ reaction.addMapping(mapping);
+ mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom3, reactantCloned.getAtom(posAtom3));
+ reaction.addMapping(mapping);
+ mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1));
+ reaction.addMapping(mapping);
+
+ IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
+ for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++)
+ reaction.addProduct(moleculeSet.getMolecule(z));
+
+ return reaction;
+ }
+
+}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java 2008-02-12 23:14:15 UTC (rev 10079)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java 2008-02-12 23:44:06 UTC (rev 10080)
@@ -24,35 +24,29 @@
*/
package org.openscience.cdk.reaction.type;
+import java.util.ArrayList;
import java.util.Iterator;
-import java.util.List;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.SingleElectron;
-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.interfaces.ISingleElectron;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
+import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism;
import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation.
- * This reaction could be represented as H-B-[c*] => [H*] + B=C. H is hydrogen atom</p>
- * <p>Make sure that the molecule has the corresponend lone pair electrons
+ * This reaction could be represented as H-B-[C*] => [H*] + B=C. H is hydrogen atom</p>
+ * <p>Make sure that the molecule has the correspond lone pair electrons
* for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
+ * <p>It is processed by the RadicalSiteIonizationMechanism class</p>
*
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -68,7 +62,7 @@
* <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 posible reactive center.</p>
+ * try to find automatically the possible reactive center.</p>
*
*
* @author Miguel Rojas
@@ -78,11 +72,12 @@
* @cdk.svnrev $Revision: 9162 $
* @cdk.set reaction-types
*
+ * @see RadicalSiteIonizationMechanism
**/
public class RadicalSiteInitiationHReaction implements IReactionProcess{
private LoggingTool logger;
private boolean hasActiveCenter;
- private CDKAtomTypeMatcher atMatcher;
+ private IReactionMechanism mechanism;
/**
* Constructor of the RadicalSiteInitiationHReaction object
@@ -90,10 +85,7 @@
*/
public RadicalSiteInitiationHReaction(){
logger = new LoggingTool(this);
- atMatcher = CDKAtomTypeMatcher.getInstance(
- NoNotificationChemObjectBuilder.getInstance(),
- CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
- );
+ mechanism = new RadicalSiteIonizationMechanism();
}
/**
* Gets the specification attribute of the RadicalSiteInitiationHReaction object
@@ -192,55 +184,19 @@
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);
- }
-
- List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(reactantCloned.getAtom(atomiP));
- reactantCloned.removeSingleElectron(selectron.get(selectron.size() -1));
-
- reactantCloned.addSingleElectron(new SingleElectron(reactantCloned.getAtom(atomkP)));
-
- BondManipulator.increaseBondOrder(reactantCloned.getBond(bondiP));
- 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);
-
+ 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);
+
+ IReaction reaction = mechanism.initiate(reactant, atomList, bondList);
+ if(reaction == null)
+ continue;
+ else
+ setOfReactions.addReaction(reaction);
}
}
}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2008-02-12 23:14:15 UTC (rev 10079)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2008-02-12 23:44:06 UTC (rev 10080)
@@ -24,35 +24,30 @@
*/
package org.openscience.cdk.reaction.type;
+import java.util.ArrayList;
import java.util.Iterator;
-import java.util.List;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.SingleElectron;
-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.interfaces.ISingleElectron;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
+import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism;
import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation.
* This reaction could be represented as A-B-[c*] => [A*] + B=C.</p>
* <p>Make sure that the molecule has the corresponend lone pair electrons
* for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
+ * <p>It is processed by the RadicalSiteIonizationMechanism class</p>
*
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -78,11 +73,12 @@
* @cdk.svnrev $Revision: 9162 $
* @cdk.set reaction-types
*
+ * @see RadicalSiteIonizationMechanism
**/
public class RadicalSiteInitiationReaction implements IReactionProcess{
private LoggingTool logger;
private boolean hasActiveCenter;
- private Object atMatcher;
+ private IReactionMechanism mechanism;
/**
* Constructor of the RadicalSiteInitiationReaction object
@@ -90,10 +86,7 @@
*/
public RadicalSiteInitiationReaction(){
logger = new LoggingTool(this);
- atMatcher = CDKAtomTypeMatcher.getInstance(
- NoNotificationChemObjectBuilder.getInstance(),
- CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
- );
+ mechanism = new RadicalSiteIonizationMechanism();
}
/**
* Gets the specification attribute of the RadicalSiteInitiationReaction object
@@ -192,55 +185,20 @@
if(atomk.getFlag(CDKConstants.REACTIVE_CENTER) && atomk.getSymbol().equals("C")
&& atomk.getFormalCharge() == 0 ){
- IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
- reaction.addReactant(reactant);
+ 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);
+
+ IReaction reaction = mechanism.initiate(reactant, atomList, bondList);
+ if(reaction == null)
+ continue;
+ else
+ setOfReactions.addReaction(reaction);
- /* 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);
- }
-
- List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(reactantCloned.getAtom(atomiP));
- reactantCloned.removeSingleElectron(selectron.get(selectron.size() -1));
-
- reactantCloned.addSingleElectron(new SingleElectron(reactantCloned.getAtom(atomkP)));
-
- BondManipulator.increaseBondOrder(reactantCloned.getBond(bondiP));
- 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);
-
}
}
}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationHReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationHReactionTest.java 2008-02-12 23:14:15 UTC (rev 10079)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationHReactionTest.java 2008-02-12 23:44:06 UTC (rev 10080)
@@ -30,6 +30,7 @@
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.Atom;
+import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
@@ -41,6 +42,8 @@
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.RadicalSiteInitiationHReaction;
@@ -68,28 +71,12 @@
*
* @return The test suite
*/
- @Test public void testAutomaticSearchCentreActiveExample1() throws Exception {
+ @Test public void testAutomaticCentreActive() throws Exception {
IReactionProcess type = new RadicalSiteInitiationHReaction();
/*[C*]-C-C*/
-// IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]([H])([H])C([H])([H])[H]");
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("C"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(0, 1, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(0, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 3, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(3, 4, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(3, 5, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(3, 6, IBond.Order.SINGLE);
+ IMolecule molecule = getMolecule();
- IAtom atom = molecule.getAtom(0);
- molecule.addSingleElectron(new SingleElectron(atom));
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
@@ -107,43 +94,208 @@
IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
/*C=C*/
-// IMolecule molecule1 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C([H])([H])=C([H])[H]");
- IMolecule molecule1 = builder.newMolecule();
- molecule1.addAtom(builder.newAtom("C"));
- molecule1.addAtom(builder.newAtom("H"));
- molecule1.addBond(0, 1, IBond.Order.SINGLE);
- molecule1.addAtom(builder.newAtom("H"));
- molecule1.addBond(0, 2, IBond.Order.SINGLE);
- molecule1.addAtom(builder.newAtom("C"));
- molecule1.addBond(0, 3, IBond.Order.DOUBLE);
- molecule1.addAtom(builder.newAtom("H"));
- molecule1.addBond(3, 4, IBond.Order.SINGLE);
- molecule1.addAtom(builder.newAtom("H"));
- molecule1.addBond(3, 5, IBond.Order.SINGLE);
+ IMolecule molecule1 = getMolecule1();
+
+ IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product1);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule1,queryAtom));
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule1,product1));
+ IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
+ /*[H*]*/
+ IMolecule molecule2 = builder.newMolecule();
+ molecule2.addAtom(new Atom("H"));
+ molecule2.addSingleElectron(new SingleElectron(molecule2.getAtom(0)));
+
+ queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,queryAtom));
+
+ }
+
+ /**
+ * A unit test suite for JUnit. Reaction: [C*]([H])([H])C([H])([H])[H] => C=C +[H*]
+ * Automatic search of the center active.
+ *
+ * @return The test suite
+ */
+ @Test public void testManuallyCentreActive() throws Exception {
+ IReactionProcess type = new RadicalSiteInitiationHReaction();
+
+ /*[C*]-C-C*/
+ IMolecule molecule = getMolecule();
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ setOfReactants.addMolecule(molecule);
+
+ /* initiate */
+ makeSureAtomTypesAreRecognized(molecule);
+
+ /*manually put the reactive center*/
+ molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(4).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(3).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ Assert.assertEquals(1, setOfReactions.getReactionCount());
+ Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());
+
+ IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+
+ /*C=C*/
+ IMolecule molecule1 = getMolecule1();
+
+ IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product1);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule1,queryAtom));
+
IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
/*[H*]*/
IMolecule molecule2 = builder.newMolecule();
molecule2.addAtom(new Atom("H"));
molecule2.addSingleElectron(new SingleElectron(molecule2.getAtom(0)));
-
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,product2));
+ queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
+ 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 RadicalSiteInitiationHReaction();
+
+ Object[] object = type.getParameters();
+ Assert.assertFalse(((Boolean) object[0]).booleanValue());
+
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+ Assert.assertTrue(((Boolean) params[0]).booleanValue());
+
+ }
+ /**
+ * A unit test suite for JUnit.
+ *
+ * @return The test suite
+ */
+ @Test public void testCDKConstants_REACTIVE_CENTER() throws Exception {
+ IReactionProcess type = new RadicalSiteInitiationHReaction();
+ IMoleculeSet setOfReactants = builder.newMoleculeSet();
+
+ IMolecule molecule = getMolecule1();
+
+ /*manually put the reactive center*/
+ molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getAtom(4).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(3).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+ setOfReactants.addMolecule(molecule);
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+
+ /* 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(3).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getAtom(4).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant.getAtom(4).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getBond(2).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant.getBond(2).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(molecule.getBond(3).getFlag(CDKConstants.REACTIVE_CENTER));
+ Assert.assertTrue(reactant.getBond(3).getFlag(CDKConstants.REACTIVE_CENTER));
+ }
+ /**
+ * A unit test suite for JUnit.
+ *
+ * @return The test suite
+ */
+ @Test public void testMapping() throws Exception {
+ IReactionProcess type = new RadicalSiteInitiationHReaction();
+
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ /*[C*]=C-C*/
+ IMolecule molecule = getMolecule1();
+ setOfReactants.addMolecule(molecule);
+
+ /*automatic looking for active center*/
+ Object[] params = {Boolean.FALSE};
+ type.setParameters(params);
+
+ /* initiate */
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+
+ Assert.assertEquals(3,setOfReactions.getReaction(0).getMappingCount());
+
Assert.assertEquals(4,setOfReactions.getReaction(0).getMappingCount());
IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(4));
- Assert.assertEquals(mappedProductA1, product2.getAtom(0));
+ Assert.assertEquals(mappedProductA1, product.getAtom(0));
IBond mappedProductB1 = (IBond)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getBond(2));
- Assert.assertEquals(mappedProductB1, product1.getBond(2));
+ Assert.assertEquals(mappedProductB1, product.getBond(2));
IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
- Assert.assertEquals(mappedProductA2, product1.getAtom(0));
+ Assert.assertEquals(mappedProductA2, product.getAtom(0));
IAtom mappedProductA3 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(3));
- Assert.assertEquals(mappedProductA3, product1.getAtom(3));
-
+ Assert.assertEquals(mappedProductA3, product.getAtom(3));
+
}
/**
+ * Get the Molecule
+ *
+ * @return The IMolecule
+ */
+ private IMolecule getMolecule() {
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(0, 2, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(0, 3, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(3, 4, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(3, 5, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(3, 6, IBond.Order.SINGLE);
+
+ IAtom atom = molecule.getAtom(0);
+ molecule.addSingleElectron(new SingleElectron(atom));
+ return molecule;
+ }
+ /**
+ * Get the Molecule 1
+ * @return The IMolecule
+ */
+ private IMolecule getMolecule1() {
+ IMolecule molecule1 = builder.newMolecule();
+ molecule1.addAtom(builder.newAtom("C"));
+ molecule1.addAtom(builder.newAtom("H"));
+ molecule1.addBond(0, 1, IBond.Order.SINGLE);
+ molecule1.addAtom(builder.newAtom("H"));
+ molecule1.addBond(0, 2, IBond.Order.SINGLE);
+ molecule1.addAtom(builder.newAtom("C"));
+ molecule1.addBond(0, 3, IBond.Order.DOUBLE);
+ molecule1.addAtom(builder.newAtom("H"));
+ molecule1.addBond(3, 4, IBond.Order.SINGLE);
+ molecule1.addAtom(builder.newAtom("H"));
+ molecule1.addBond(3, 5, IBond.Order.SINGLE);
+ return molecule1;
+ }
+
+ /**
* Test to recognize if a IMolecule matcher correctly the CDKAtomTypes.
*
* @param molecule The IMolecule to analyze
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationReactionTest.java 2008-02-12 23:14:15 UTC (rev 10079)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/RadicalSiteInitiationReactionTest.java 2008-02-12 23:44:06 UTC (rev 10080)
@@ -29,6 +29,7 @@
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.SingleElectron;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
@@ -40,6 +41,8 @@
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
+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.type.RadicalSiteInitiationReaction;
@@ -68,24 +71,10 @@
*
* @return The test suite
*/
- @Test public void testAutomaticSearchCentreActiveExample1() throws Exception {
+ @Test public void testAutomaticCentreActive() throws Exception {
IReactionProcess type = new RadicalSiteInitiationReaction();
/*[C*]-C-C*/
-// IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]-C-C");
- 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.SINGLE);
-
- addExplicitHydrogens(molecule);
- IAtom atom = molecule.getAtom(0);
- molecule.addSingleElectron(new SingleElectron(atom));
- atom.setFormalCharge(0);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
- makeSureAtomTypesAreRecognized(molecule);
+ IMolecule molecule = getMolecule();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
@@ -103,19 +92,19 @@
IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
/*C=C*/
-// IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C=C");
IMolecule molecule1 = builder.newMolecule();
molecule1.addAtom(builder.newAtom("C"));
molecule1.addAtom(builder.newAtom("C"));
molecule1.addBond(0, 1, IBond.Order.DOUBLE);
addExplicitHydrogens(molecule1);
-
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule1,product1));
+
+
+ QueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product1);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule1,queryAtom));
IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
/*[C*]*/
-// molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]");
IMolecule molecule2 = builder.newMolecule();
molecule2.addAtom(builder.newAtom("C"));
molecule2.addAtom(builder.newAtom("H"));
@@ -124,23 +113,132 @@
molecule2.addBond(0, 2, IBond.Order.SINGLE);
molecule2.addAtom(builder.newAtom("H"));
molecule2.addBond(0, 3, IBond.Order.SINGLE);
- atom = molecule2.getAtom(0);
+ IAtom atom = molecule2.getAtom(0);
molecule2.addSingleElectron(new SingleElectron(atom));
-
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,product2));
- Assert.assertEquals(4,setOfReactions.getReaction(0).getMappingCount());
- IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(2));
- Assert.assertEquals(mappedProductA1, product2.getAtom(0));
+
+ queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
+ 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 RadicalSiteInitiationReaction();
+
+ Object[] object = type.getParameters();
+ Assert.assertFalse(((Boolean) object[0]).booleanValue());
+
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+ Assert.assertTrue(((Boolean) params[0]).booleanValue());
+
+ }
+ /**
+ * A unit test suite for JUnit.
+ *
+ * @return The test suite
+ */
+ @Test public void testCDKConstants_REACTIVE_CENTER() throws Exception {
+ IReactionProcess type = new RadicalSiteInitiationReaction();
+ IMoleculeSet setOfReactants = builder.newMoleculeSet();
+
+ IMolecule molecule = getMolecule();
+
+ /*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);
+
+ setOfReactants.addMolecule(molecule);
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+
+ /* 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 RadicalSiteInitiationReaction();
+
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ /*[C*]=C-C*/
+ IMolecule molecule = getMolecule();
+
+ 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);
+
+ setOfReactants.addMolecule(molecule);
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+
+ /* initiate */
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+ IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
+
+ Assert.assertEquals(4,setOfReactions.getReaction(0).getMappingCount());
+ 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(0));
Assert.assertEquals(mappedProductB1, product1.getBond(0));
- IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
- Assert.assertEquals(mappedProductA2, product1.getAtom(0));
- IAtom mappedProductA3 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(1));
- Assert.assertEquals(mappedProductA3, product1.getAtom(1));
-
+ IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(2));
+ Assert.assertEquals(mappedProductA2, product2.getAtom(0));
+ IAtom mappedProductA3 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
+ Assert.assertEquals(mappedProductA3, product1.getAtom(0));
+
}
/**
+ * Get the IMolecule
+ *
+ * @return The IMolecule
+ * @throws Exception
+ */
+ private IMolecule getMolecule() 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.SINGLE);
+
+ addExplicitHydrogens(molecule);
+ IAtom atom = molecule.getAtom(0);
+ molecule.addSingleElectron(new SingleElectron(atom));
+ atom.setFormalCharge(0);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ makeSureAtomTypesAreRecognized(molecule);
+ return molecule;
+ }
+ /**
* Test to recognize if a IMolecule matcher correctly the CDKAtomTypes.
*
* @param molecule The IMolecule to analyze
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