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[Cdk-commits] SF.net SVN: cdk: [10093] branches/miguelrojasch/reaction/src/org/ openscience/cdk
|
From: <mig...@us...> - 2008-02-13 23:18:15
|
Revision: 10093
http://cdk.svn.sourceforge.net/cdk/?rev=10093&view=rev
Author: miguelrojasch
Date: 2008-02-13 15:18:13 -0800 (Wed, 13 Feb 2008)
Log Message:
-----------
changed name of the class BrekingBond* to HeterolyticCleavage*
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/atomtype/ReactionStructuresTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MreactionTests.java
Added Paths:
-----------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HeterolyticCleavageReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/HeterolyticCleavageReactionTest.java
Removed Paths:
-------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -38,7 +38,7 @@
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
-import org.openscience.cdk.reaction.type.BreakingBondReaction;
+import org.openscience.cdk.reaction.type.HeterolyticCleavageReaction;
import org.openscience.cdk.reaction.type.HyperconjugationReaction;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.StructureResonanceGenerator;
@@ -297,7 +297,7 @@
*/
private IAtomContainerSet getHyperconjugationInteractions(IAtomContainer ac, IAtomContainerSet iSet) throws IOException, ClassNotFoundException, CDKException {
IAtomContainerSet set = ac.getBuilder().newAtomContainerSet();
- IReactionProcess type = new BreakingBondReaction();
+ IReactionProcess type = new HeterolyticCleavageReaction();
cleanFlagReactiveCenter(ac);
boolean found = false; /* control obtained containers */
IMoleculeSet setOfReactants = ac.getBuilder().newMoleculeSet();
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -50,7 +50,7 @@
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IntegerResult;
-import org.openscience.cdk.reaction.type.BreakingBondReaction;
+import org.openscience.cdk.reaction.type.HeterolyticCleavageReaction;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.StructureResonanceGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -181,7 +181,7 @@
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),dar);
}
- BreakingBondReaction type = new BreakingBondReaction();
+ HeterolyticCleavageReaction type = new HeterolyticCleavageReaction();
Object[] paramsR = {Boolean.TRUE};
type.setParameters(paramsR);
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -1,147 +0,0 @@
-/* $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 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.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.nonotify.NoNotificationChemObjectBuilder;
-import org.openscience.cdk.reaction.IReactionMechanism;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
-
-/**
- * This mechanism displaces the chemical bond to an Atom. Generating one with
- * excess charge and the other with deficiency.
- * It returns the reaction mechanism which has been cloned the IMolecule.
- *
- * @author miguelrojasch
- * @cdk.created 2008-02-10
- * @cdk.module reaction
- *
- */
-public class BreakingBondMechanism implements IReactionMechanism{
-
- private CDKAtomTypeMatcher atMatcher;
-
- /**
- * Constructor of the BreakingBondMechanism object.
- *
- */
- public BreakingBondMechanism(){
- 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 moleculeSet The IMolecule to apply the mechanism
- * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms.
- * The first atom receives the positive charge charge and the second
- * negative charge
- * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond
- * @return The Reaction mechanism
- *
- */
- public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
- if (moleculeSet.getMoleculeCount() != 1) {
- throw new CDKException("TautomerizationMechanism only expects one IMolecule");
- }
- if (atomList.size() != 2) {
- throw new CDKException("BreakingBondMechanism expects two atoms in the ArrayList");
- }
- if (bondList.size() != 1) {
- throw new CDKException("BreakingBondMechanism only expect one bond in the ArrayList");
- }
- IMolecule molecule = moleculeSet.getMolecule(0);
- IMolecule reactantCloned;
- try {
- reactantCloned = (IMolecule) molecule.clone();
- } catch (CloneNotSupportedException e) {
- throw new CDKException("Could not clone IMolecule!", e);
- }
- IAtom atom1 = atomList.get(0);
- int posAtom1 = molecule.getAtomNumber(atom1);
- IAtom atom2 = atomList.get(1);
- int posAtom2 = molecule.getAtomNumber(atom2);
- IBond bond1 = bondList.get(0);
- int posBond1 = molecule.getBondNumber(bond1);
-
- if(bond1.getOrder() == IBond.Order.SINGLE)
- reactantCloned.removeBond(reactantCloned.getBond(posBond1));
- else
- BondManipulator.decreaseBondOrder(reactantCloned.getBond(posBond1));
-
- int charge = reactantCloned.getAtom(posAtom1).getFormalCharge();
- reactantCloned.getAtom(posAtom1).setFormalCharge(charge+1);
- // check if resulting atom type is reasonable
- reactantCloned.getAtom(posAtom1).setHybridization(null);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
- IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom1));
- if (type == null) return null;
-
- charge = reactantCloned.getAtom(posAtom2).getFormalCharge();
- reactantCloned.getAtom(posAtom2).setFormalCharge(charge-1);
- reactantCloned.addLonePair(new LonePair(reactantCloned.getAtom(posAtom2)));
- // check if resulting atom type is reasonable: an acceptor atom cannot be charged positive*/
- reactantCloned.getAtom(posAtom2).setHybridization(null);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
- type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom2));
- 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);
- if(bond1.getOrder() != IBond.Order.SINGLE) {
- mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1));
- reaction.addMapping(mapping);
- reaction.addProduct(reactantCloned);
- } else{
- IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
- for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){
- reaction.addProduct(moleculeSetP.getMolecule(z));
- }
- }
-
- return reaction;
- }
-
-}
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java (from rev 10088, branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -0,0 +1,147 @@
+/* $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 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.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.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.reaction.IReactionMechanism;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.BondManipulator;
+
+/**
+ * This mechanism displaces the chemical bond to an Atom. Generating one with
+ * excess charge and the other with deficiency.
+ * It returns the reaction mechanism which has been cloned the IMolecule.
+ *
+ * @author miguelrojasch
+ * @cdk.created 2008-02-10
+ * @cdk.module reaction
+ *
+ */
+public class HeterolyticCleavageMechanism implements IReactionMechanism{
+
+ private CDKAtomTypeMatcher atMatcher;
+
+ /**
+ * Constructor of the HeterolyticCleavageMechanism object.
+ *
+ */
+ public HeterolyticCleavageMechanism(){
+ 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 moleculeSet The IMolecule to apply the mechanism
+ * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms.
+ * The first atom receives the positive charge charge and the second
+ * negative charge
+ * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond
+ * @return The Reaction mechanism
+ *
+ */
+ public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
+ if (moleculeSet.getMoleculeCount() != 1) {
+ throw new CDKException("TautomerizationMechanism only expects one IMolecule");
+ }
+ if (atomList.size() != 2) {
+ throw new CDKException("HeterolyticCleavageMechanism expects two atoms in the ArrayList");
+ }
+ if (bondList.size() != 1) {
+ throw new CDKException("HeterolyticCleavageMechanism only expect one bond in the ArrayList");
+ }
+ IMolecule molecule = moleculeSet.getMolecule(0);
+ IMolecule reactantCloned;
+ try {
+ reactantCloned = (IMolecule) molecule.clone();
+ } catch (CloneNotSupportedException e) {
+ throw new CDKException("Could not clone IMolecule!", e);
+ }
+ IAtom atom1 = atomList.get(0);
+ int posAtom1 = molecule.getAtomNumber(atom1);
+ IAtom atom2 = atomList.get(1);
+ int posAtom2 = molecule.getAtomNumber(atom2);
+ IBond bond1 = bondList.get(0);
+ int posBond1 = molecule.getBondNumber(bond1);
+
+ if(bond1.getOrder() == IBond.Order.SINGLE)
+ reactantCloned.removeBond(reactantCloned.getBond(posBond1));
+ else
+ BondManipulator.decreaseBondOrder(reactantCloned.getBond(posBond1));
+
+ int charge = reactantCloned.getAtom(posAtom1).getFormalCharge();
+ reactantCloned.getAtom(posAtom1).setFormalCharge(charge+1);
+ // check if resulting atom type is reasonable
+ reactantCloned.getAtom(posAtom1).setHybridization(null);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
+ IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom1));
+ if (type == null) return null;
+
+ charge = reactantCloned.getAtom(posAtom2).getFormalCharge();
+ reactantCloned.getAtom(posAtom2).setFormalCharge(charge-1);
+ reactantCloned.addLonePair(new LonePair(reactantCloned.getAtom(posAtom2)));
+ // check if resulting atom type is reasonable: an acceptor atom cannot be charged positive*/
+ reactantCloned.getAtom(posAtom2).setHybridization(null);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
+ type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom2));
+ 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);
+ if(bond1.getOrder() != IBond.Order.SINGLE) {
+ mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1));
+ reaction.addMapping(mapping);
+ reaction.addProduct(reactantCloned);
+ } else{
+ IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
+ for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){
+ reaction.addProduct(moleculeSetP.getMolecule(z));
+ }
+ }
+
+ return reaction;
+ }
+
+}
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -1,259 +0,0 @@
-/*
- * $RCSfile$
- * $Author: egonw $
- * $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
- * $Revision: 5855 $
- *
- * Copyright (C) 2006-2007 Miguel Rojas <mig...@un...>
- *
- * 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.type;
-
-
-import java.util.ArrayList;
-import java.util.Iterator;
-
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IBond;
-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.reaction.IReactionMechanism;
-import org.openscience.cdk.reaction.IReactionProcess;
-import org.openscience.cdk.reaction.ReactionSpecification;
-import org.openscience.cdk.reaction.mechanism.BreakingBondMechanism;
-import org.openscience.cdk.tools.LoggingTool;
-
-/**
- * <p>IReactionProcess which a bond is broken displacing the electron to one of the
- * atoms. The mechanism will produce one atom with excess of charge and the other one deficiency.
- * Depending of the bond order, the bond will be removed or simply the order decreased.
- * As there are two directions for displacing a bond in a polar manner,
- * each case is investigated twice:</p>
- *
- * <pre>A-B => [A+] + |[B-]</pre>
- * <pre>A-B => |[A-] + [B+]</pre>
- *
- * <p>It will not be created structures no possible, e.g; C=O => [C-][O+].</p>
- * <p>Below you have an example how to initiate the mechanism.</p>
- * <p>It is processed by the BreakingBondMechanism class</p>
- * <pre>
- * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
- * setOfReactants.addMolecule(new Molecule());
- * IReactionProcess type = new BreakingBondReaction();
- * Object[] params = {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 specify 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 specified then the reaction process will
- * try to find automatically the possible reaction centers.</p>
- *
- *
- * @author Miguel Rojas
- *
- * @cdk.created 2006-06-09
- * @cdk.module reaction
- * @cdk.svnrev $Revision: 9162 $
- * @cdk.set reaction-types
- *
- * @see BreakingBondMechanism
- **/
-public class BreakingBondReaction implements IReactionProcess{
- private LoggingTool logger;
- private boolean hasActiveCenter;
- private IReactionMechanism mechanism;
-
- /**
- * Constructor of the BreakingBondReaction object.
- *
- */
- public BreakingBondReaction(){
- logger = new LoggingTool(this);
- mechanism = new BreakingBondMechanism();
- }
-
- /**
- * Gets the specification attribute of the BreakingBondReaction object.
- *
- *@return The specification value
- */
- public ReactionSpecification getSpecification() {
- return new ReactionSpecification(
- "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#BreakingBondReaction",
- this.getClass().getName(),
- "$Id: BreakingBondReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
- "The Chemistry Development Kit");
- }
-
- /**
- * Sets the parameters attribute of the BreakingBondReaction object.
- *
- * @param params The parameter is if the molecule has already fixed the center active or not. It
- * should be set before to initiate the reaction with a setFlag: CDKConstants.REACTIVE_CENTER
- *@exception CDKException Description of the Exception
- */
- public void setParameters(Object[] params) throws CDKException {
- if (params.length > 1) {
- throw new CDKException("BreakingBondReaction only expects one parameter");
- }
- if (!(params[0] instanceof Boolean)) {
- throw new CDKException("The parameter 1 must be of type boolean");
- }
- hasActiveCenter = ((Boolean) params[0]).booleanValue();
- }
-
-
- /**
- * Gets the parameters attribute of the BreakingBondReaction object.
- *
- *@return The parameters value
- */
- public Object[] getParameters() {
- Object[] params = new Object[1];
- params[0] = new Boolean (hasActiveCenter);
- return params;
- }
-
- /**
- * Initiate process.
- * It is needed to call the addExplicitHydrogensToSatisfyValency
- * from the class tools.HydrogenAdder.
- *
- *@param reactants reactants of the reaction
- *@param agents agents of the reaction (Must be in this case null)
- *
- *@exception CDKException Description of the Exception
- */
- public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
-
- logger.debug("initiate reaction: BreakingBondReaction");
-
- if (reactants.getMoleculeCount() != 1) {
- throw new CDKException("BreakingBondReaction only expects one reactant");
- }
- if (agents != null) {
- throw new CDKException("BreakingBondReaction don't expects agents");
- }
-
- IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
- IMolecule reactant = reactants.getMolecule(0);
-
- /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
- if(!hasActiveCenter){
- setActiveCenters(reactant);
- }
-
- Iterator<IBond> bondis = reactant.bonds();
- while (bondis.hasNext()) {
- IBond bondi = bondis.next();
-
- if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)) {
- int chargeAtom0 = bondi.getAtom(0).getFormalCharge() == null ? 0 : bondi.getAtom(0).getFormalCharge();
- int chargeAtom1 = bondi.getAtom(1).getFormalCharge() == null ? 0 : bondi.getAtom(1).getFormalCharge();
- if(chargeAtom0 >= 0 && chargeAtom1 >= 0){
-
- /**/
- for (int j = 0; j < 2; j++){
-
- ArrayList<IAtom> atomList = new ArrayList<IAtom>();
- if (j == 0){
- atomList.add(bondi.getAtom(0));
- atomList.add(bondi.getAtom(1));
- }else{
- atomList.add(bondi.getAtom(1));
- atomList.add(bondi.getAtom(0));
- }
- ArrayList<IBond> bondList = new ArrayList<IBond>();
- bondList.add(bondi);
-
- IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
- moleculeSet.addMolecule(reactant);
- IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
- if(reaction == null)
- continue;
- else
- setOfReactions.addReaction(reaction);
-
- }
-
- }
-
- }
- }
-
- return setOfReactions;
- }
- /**
- * set the active center for this molecule.
- * The active center will be those which correspond with A-B. If
- * the bond is simple, it will be broken forming two fragments
- * <pre>
- * A: Atom
- * #/=/-: bond
- * B: Atom
- * </pre>
- *
- * @param reactant The molecule to set the activity
- * @throws CDKException
- */
- private void setActiveCenters(IMolecule reactant) throws CDKException {
- Iterator<IBond> bonds = reactant.bonds();
- while (bonds.hasNext()) {
- IBond bond = (IBond) bonds.next();
- int chargeAtom0 = bond.getAtom(0).getFormalCharge() == null ? 0 : bond.getAtom(0).getFormalCharge();
- int chargeAtom1 = bond.getAtom(1).getFormalCharge() == null ? 0 : bond.getAtom(1).getFormalCharge();
- if(chargeAtom0 >= 0 && chargeAtom1 >= 0) {
- IAtom atom1 = bond.getAtom(0);
- IAtom atom2 = bond.getAtom(1);
- atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
- atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
- bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
- }
- }
- }
- /**
- * Gets the parameterNames attribute of the BreakingBondReaction object.
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "hasActiveCenter";
- return params;
- }
-
-
- /**
- * Gets the parameterType attribute of the BreakingBondReaction object.
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- return new Boolean(false);
- }
-}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -38,7 +38,7 @@
import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
-import org.openscience.cdk.reaction.mechanism.BreakingBondMechanism;
+import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -46,7 +46,7 @@
* This reaction could be represented as RC-C#[O+] => R[C] + |C#[O+]</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 BreakingBondMechanism class</p>
+ * <p>It is processed by the HeterolyticCleavageMechanism class</p>
*
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -72,7 +72,7 @@
* @cdk.svnrev $Revision: 9162 $
* @cdk.set reaction-types
*
- * @see BreakingBondMechanism
+ * @see HeterolyticCleavageMechanism
**/
public class CarbonylEliminationReaction implements IReactionProcess{
private LoggingTool logger;
@@ -85,7 +85,7 @@
*/
public CarbonylEliminationReaction(){
logger = new LoggingTool(this);
- mechanism = new BreakingBondMechanism();
+ mechanism = new HeterolyticCleavageMechanism();
}
/**
* Gets the specification attribute of the CarbonylEliminationReaction object.
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -40,7 +40,7 @@
import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
-import org.openscience.cdk.reaction.mechanism.BreakingBondMechanism;
+import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -48,7 +48,7 @@
* <p>IReactionProcess which participate in movement resonance.
* This reaction could be represented as two forms</p>
* <pre>X=A => |[X-]-[A+]. X represents an acceptor atomType.
- * <p>It is processed by the BreakingBondMechanism class</p>
+ * <p>It is processed by the HeterolyticCleavageMechanism class</p>
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
@@ -73,7 +73,7 @@
* @cdk.svnrev $Revision: 9162 $
* @cdk.set reaction-types
*
- * @see BreakingBondMechanism
+ * @see HeterolyticCleavageMechanism
**/
public class DisplacementChargeFromAcceptorReaction implements IReactionProcess{
private LoggingTool logger;
@@ -86,7 +86,7 @@
*/
public DisplacementChargeFromAcceptorReaction(){
logger = new LoggingTool(this);
- mechanism = new BreakingBondMechanism();
+ mechanism = new HeterolyticCleavageMechanism();
}
/**
* Gets the specification attribute of the DisplacementChargeFromAcceptorReaction object
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HeterolyticCleavageReaction.java (from rev 10088, branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HeterolyticCleavageReaction.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HeterolyticCleavageReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -0,0 +1,259 @@
+/*
+ * $RCSfile$
+ * $Author: egonw $
+ * $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
+ * $Revision: 5855 $
+ *
+ * Copyright (C) 2006-2007 Miguel Rojas <mig...@un...>
+ *
+ * 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.type;
+
+
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IBond;
+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.reaction.IReactionMechanism;
+import org.openscience.cdk.reaction.IReactionProcess;
+import org.openscience.cdk.reaction.ReactionSpecification;
+import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism;
+import org.openscience.cdk.tools.LoggingTool;
+
+/**
+ * <p>IReactionProcess which a bond is broken displacing the electron to one of the
+ * atoms. The mechanism will produce one atom with excess of charge and the other one deficiency.
+ * Depending of the bond order, the bond will be removed or simply the order decreased.
+ * As there are two directions for displacing a bond in a polar manner,
+ * each case is investigated twice:</p>
+ *
+ * <pre>A-B => [A+] + |[B-]</pre>
+ * <pre>A-B => |[A-] + [B+]</pre>
+ *
+ * <p>It will not be created structures no possible, e.g; C=O => [C-][O+].</p>
+ * <p>Below you have an example how to initiate the mechanism.</p>
+ * <p>It is processed by the HeterolyticCleavageMechanism class</p>
+ * <pre>
+ * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ * setOfReactants.addMolecule(new Molecule());
+ * IReactionProcess type = new HeterolyticCleavageReaction();
+ * Object[] params = {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 specify 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 specified then the reaction process will
+ * try to find automatically the possible reaction centers.</p>
+ *
+ *
+ * @author Miguel Rojas
+ *
+ * @cdk.created 2006-06-09
+ * @cdk.module reaction
+ * @cdk.svnrev $Revision: 9162 $
+ * @cdk.set reaction-types
+ *
+ * @see HeterolyticCleavageMechanism
+ **/
+public class HeterolyticCleavageReaction implements IReactionProcess{
+ private LoggingTool logger;
+ private boolean hasActiveCenter;
+ private IReactionMechanism mechanism;
+
+ /**
+ * Constructor of the HeterolyticCleavageReaction object.
+ *
+ */
+ public HeterolyticCleavageReaction(){
+ logger = new LoggingTool(this);
+ mechanism = new HeterolyticCleavageMechanism();
+ }
+
+ /**
+ * Gets the specification attribute of the HeterolyticCleavageReaction object.
+ *
+ *@return The specification value
+ */
+ public ReactionSpecification getSpecification() {
+ return new ReactionSpecification(
+ "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#BreakingBondReaction",
+ this.getClass().getName(),
+ "$Id: HeterolyticCleavageReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
+ "The Chemistry Development Kit");
+ }
+
+ /**
+ * Sets the parameters attribute of the HeterolyticCleavageReaction object.
+ *
+ * @param params The parameter is if the molecule has already fixed the center active or not. It
+ * should be set before to initiate the reaction with a setFlag: CDKConstants.REACTIVE_CENTER
+ *@exception CDKException Description of the Exception
+ */
+ public void setParameters(Object[] params) throws CDKException {
+ if (params.length > 1) {
+ throw new CDKException("HeterolyticCleavageReaction only expects one parameter");
+ }
+ if (!(params[0] instanceof Boolean)) {
+ throw new CDKException("The parameter 1 must be of type boolean");
+ }
+ hasActiveCenter = ((Boolean) params[0]).booleanValue();
+ }
+
+
+ /**
+ * Gets the parameters attribute of the HeterolyticCleavageReaction object.
+ *
+ *@return The parameters value
+ */
+ public Object[] getParameters() {
+ Object[] params = new Object[1];
+ params[0] = new Boolean (hasActiveCenter);
+ return params;
+ }
+
+ /**
+ * Initiate process.
+ * It is needed to call the addExplicitHydrogensToSatisfyValency
+ * from the class tools.HydrogenAdder.
+ *
+ *@param reactants reactants of the reaction
+ *@param agents agents of the reaction (Must be in this case null)
+ *
+ *@exception CDKException Description of the Exception
+ */
+ public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
+
+ logger.debug("initiate reaction: HeterolyticCleavageReaction");
+
+ if (reactants.getMoleculeCount() != 1) {
+ throw new CDKException("HeterolyticCleavageReaction only expects one reactant");
+ }
+ if (agents != null) {
+ throw new CDKException("HeterolyticCleavageReaction don't expects agents");
+ }
+
+ IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
+ IMolecule reactant = reactants.getMolecule(0);
+
+ /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
+ if(!hasActiveCenter){
+ setActiveCenters(reactant);
+ }
+
+ Iterator<IBond> bondis = reactant.bonds();
+ while (bondis.hasNext()) {
+ IBond bondi = bondis.next();
+
+ if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)) {
+ int chargeAtom0 = bondi.getAtom(0).getFormalCharge() == null ? 0 : bondi.getAtom(0).getFormalCharge();
+ int chargeAtom1 = bondi.getAtom(1).getFormalCharge() == null ? 0 : bondi.getAtom(1).getFormalCharge();
+ if(chargeAtom0 >= 0 && chargeAtom1 >= 0){
+
+ /**/
+ for (int j = 0; j < 2; j++){
+
+ ArrayList<IAtom> atomList = new ArrayList<IAtom>();
+ if (j == 0){
+ atomList.add(bondi.getAtom(0));
+ atomList.add(bondi.getAtom(1));
+ }else{
+ atomList.add(bondi.getAtom(1));
+ atomList.add(bondi.getAtom(0));
+ }
+ ArrayList<IBond> bondList = new ArrayList<IBond>();
+ bondList.add(bondi);
+
+ IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
+ moleculeSet.addMolecule(reactant);
+ IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
+ if(reaction == null)
+ continue;
+ else
+ setOfReactions.addReaction(reaction);
+
+ }
+
+ }
+
+ }
+ }
+
+ return setOfReactions;
+ }
+ /**
+ * set the active center for this molecule.
+ * The active center will be those which correspond with A-B. If
+ * the bond is simple, it will be broken forming two fragments
+ * <pre>
+ * A: Atom
+ * #/=/-: bond
+ * B: Atom
+ * </pre>
+ *
+ * @param reactant The molecule to set the activity
+ * @throws CDKException
+ */
+ private void setActiveCenters(IMolecule reactant) throws CDKException {
+ Iterator<IBond> bonds = reactant.bonds();
+ while (bonds.hasNext()) {
+ IBond bond = (IBond) bonds.next();
+ int chargeAtom0 = bond.getAtom(0).getFormalCharge() == null ? 0 : bond.getAtom(0).getFormalCharge();
+ int chargeAtom1 = bond.getAtom(1).getFormalCharge() == null ? 0 : bond.getAtom(1).getFormalCharge();
+ if(chargeAtom0 >= 0 && chargeAtom1 >= 0) {
+ IAtom atom1 = bond.getAtom(0);
+ IAtom atom2 = bond.getAtom(1);
+ atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
+ atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
+ bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
+ }
+ }
+ }
+ /**
+ * Gets the parameterNames attribute of the HeterolyticCleavageReaction object.
+ *
+ *@return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ String[] params = new String[1];
+ params[0] = "hasActiveCenter";
+ return params;
+ }
+
+
+ /**
+ * Gets the parameterType attribute of the HeterolyticCleavageReaction object.
+ *
+ *@param name Description of the Parameter
+ *@return The parameterType value
+ */
+ public Object getParameterType(String name) {
+ return new Boolean(false);
+ }
+}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -150,7 +150,7 @@
*/
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
- logger.debug("initiate reaction: BreakingBondReaction");
+ logger.debug("initiate reaction: HeterolyticCleavageReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("PiBondingMovementReaction only expects one reactant");
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -51,7 +51,7 @@
* <pre>X=Y-Z-H => X(H)-Y=Z</pre>
*
* <p>Below you have an example how to initiate the mechanism.</p>
- * <p>It is processed by the BreakingBondMechanism class</p>
+ * <p>It is processed by the HeterolyticCleavageMechanism class</p>
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/atomtype/ReactionStructuresTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/atomtype/ReactionStructuresTest.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/atomtype/ReactionStructuresTest.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -31,7 +31,7 @@
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.test.NewCDKTestCase;
-import org.openscience.cdk.test.reaction.type.BreakingBondReactionTest;
+import org.openscience.cdk.test.reaction.type.HeterolyticCleavageReactionTest;
import org.openscience.cdk.test.reaction.type.CleavageBondReactionTest;
import org.openscience.cdk.test.reaction.type.RearrangementRadical3ReactionTest;
@@ -107,7 +107,7 @@
* A unit test suite for JUnit. Compound and his fragments to be tested
* @throws Exception
*
- * @see BreakingBondReactionTest#testCspSingleB()
+ * @see HeterolyticCleavageReactionTest#testCspSingleB()
*/
@Test public void testM4() throws Exception {
//Smiles("C#[C+]")
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MreactionTests.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MreactionTests.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MreactionTests.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -33,7 +33,7 @@
import org.openscience.cdk.test.reaction.type.AdductionProtonLPReactionTest;
import org.openscience.cdk.test.reaction.type.AdductionProtonPBReactionTest;
import org.openscience.cdk.test.reaction.type.AdductionSodiumLPReactionTest;
-import org.openscience.cdk.test.reaction.type.BreakingBondReactionTest;
+import org.openscience.cdk.test.reaction.type.HeterolyticCleavageReactionTest;
import org.openscience.cdk.test.reaction.type.CarbonylEliminationReactionTest;
import org.openscience.cdk.test.reaction.type.CleavageBondMultiReactionTest;
import org.openscience.cdk.test.reaction.type.CleavageBondReactionTest;
@@ -84,7 +84,7 @@
suite.addTest(new JUnit4TestAdapter(AdductionProtonLPReactionTest.class));
suite.addTest(new JUnit4TestAdapter(AdductionProtonPBReactionTest.class));
suite.addTest(new JUnit4TestAdapter(AdductionSodiumLPReactionTest.class));
- suite.addTest(new JUnit4TestAdapter(BreakingBondReactionTest.class));
+ suite.addTest(new JUnit4TestAdapter(HeterolyticCleavageReactionTest.class));
suite.addTest(new JUnit4TestAdapter(CarbonylEliminationReactionTest.class));
suite.addTest(new JUnit4TestAdapter(CleavageBondReactionTest.class));
suite.addTest(new JUnit4TestAdapter(CleavageBondMultiReactionTest.class));
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java 2008-02-13 22:38:46 UTC (rev 10092)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java 2008-02-13 23:18:13 UTC (rev 10093)
@@ -1,1861 +0,0 @@
-/* $RCSfile$
- * $Author: miguelrojasch $
- * $Date: 2006-05-11 14:25:07 +0200 (Do, 11 Mai 2006) $
- * $Revision: 6221 $
- *
- * Copyright (C) 2004-2007 Miguel Rojas <mig...@un...>
- *
- * 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.test.reaction.type;
-
-
-import java.util.Iterator;
-
-import org.junit.Assert;
-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.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.type.BreakingBondReaction;
-import org.openscience.cdk.smiles.SmilesGenerator;
-import org.openscience.cdk.test.reaction.ReactionProcessTest;
-import org.openscience.cdk.tools.LonePairElectronChecker;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.tools.manipulator.ReactionManipulator;
-
-/**
- * TestSuite that runs a test for the BreakingBondReactionTest.
- * Generalized Reaction: A=B => |[A-]-[B+] + [A+]-|[B-]. Depending of the bond order
- * the bond will be removed or simply the order decreased.
- *
- * @cdk.module test-reaction
- */
-public class BreakingBondReactionTest extends ReactionProcessTest {
-
- private final static IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
- private final static LonePairElectronChecker lpcheck = new LonePairElectronChecker();
- /**
- * The JUnit setup method
- */
- @BeforeClass public static void setUp() throws Exception {
- setReaction(BreakingBondReaction.class);
- }
- /**
- * A unit test suite for JUnit. Reaction: propane.
- * CC!-!C => C[C+] + [C-]
- * C[C-] + [C+]
- *
- * @cdk.inchi InChI=1/C3H8/c1-3-2/h3H2,1-2H3
- *
- * @return The test suite
- */
- @Test public void testCsp3SingleB() throws Exception {
- //Smiles("CCC")
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("C"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.SINGLE);
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(0, 3, IBond.Order.SINGLE);
- molecule.addBond(0, 4, IBond.Order.SINGLE);
- molecule.addBond(0, 5, IBond.Order.SINGLE);
- molecule.addBond(1, 6, IBond.Order.SINGLE);
- molecule.addBond(1, 7, IBond.Order.SINGLE);
- molecule.addBond(2, 8, IBond.Order.SINGLE);
- molecule.addBond(2, 9, IBond.Order.SINGLE);
- molecule.addBond(2, 10, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-
- molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
- molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
- molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
-
- IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
- setOfReactants.addMolecule(molecule);
-
- IReactionProcess type = new BreakingBondReaction();
- Object[] params = {Boolean.TRUE};
- type.setParameters(params);
-
- /* initiate */
- IReactionSet setOfReactions = type.initiate(setOfReactants, null);
-
- Assert.assertEquals(2, setOfReactions.getReactionCount());
-
- // expected products
-
- //Smiles("C[C+]")
- IMolecule expected1 = builder.newMolecule();
- expected1.addAtom(builder.newAtom("C"));
- expected1.addAtom(builder.newAtom("C"));
- expected1.getAtom(1).setFormalCharge(+1);
- expected1.addBond(0, 1, IBond.Order.SINGLE);
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addBond(0, 2, IBond.Order.SINGLE);
- expected1.addBond(0, 3, IBond.Order.SINGLE);
- expected1.addBond(0, 4, IBond.Order.SINGLE);
- expected1.addBond(1, 5, IBond.Order.SINGLE);
- expected1.addBond(1, 6, IBond.Order.SINGLE);;
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected1);
- IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
- IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected1);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product1,queryAtom));
-
- //Smiles("[C-]")
- IMolecule expected2 = builder.newMolecule();
- expected2.addAtom(builder.newAtom("C"));
- expected2.getAtom(0).setFormalCharge(-1);
- expected2.addAtom(builder.newAtom("H"));
- expected2.addAtom(builder.newAtom("H"));
- expected2.addAtom(builder.newAtom("H"));
- expected2.addBond(0, 1, IBond.Order.SINGLE);
- expected2.addBond(0, 2, IBond.Order.SINGLE);
- expected2.addBond(0, 3, IBond.Order.SINGLE);
-
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected2);
- lpcheck.saturate(expected2);
- IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected2);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product2,queryAtom));
-
- //Smiles("C[C-]")
- expected1.getAtom(1).setFormalCharge(-1);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected1);
- product1 = setOfReactions.getReaction(1).getProducts().getMolecule(0);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected1);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product1,queryAtom));
-
- //Smiles("[C+]")
- expected2.getAtom(0).setFormalCharge(+1);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected2);
- product2 = setOfReactions.getReaction(1).getProducts().getMolecule(1);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected2);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product2,queryAtom));
- }
- /**
- * A unit test suite for JUnit. Reaction: .
- * C[C+]!-!C => CC + [C+]
- *
- * @return The test suite
- */
- @Test public void testCsp2ChargeSingleB() throws Exception {
-
- }
- /**
- * A unit test suite for JUnit. Reaction: Propene.
- * C=C!-!C => C=[C+] + [C-]
- * C=[C-] + [C+]
- *
- * @cdk.inchi InChI=1/C3H6/c1-3-2/h3H,1H2,2H3
- *
- * @return The test suite
- */
- @Test public void testCsp2SingleB() throws Exception {
- //Smiles("C=CC")
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("C"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.DOUBLE);
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(0, 3, IBond.Order.SINGLE);
- molecule.addBond(0, 4, IBond.Order.SINGLE);
- molecule.addBond(1, 5, IBond.Order.SINGLE);
- molecule.addBond(2, 6, IBond.Order.SINGLE);
- molecule.addBond(2, 7, IBond.Order.SINGLE);
- molecule.addBond(2, 8, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-
- molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
- molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
- molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
-
- IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
- setOfReactants.addMolecule(molecule);
-
- IReactionProcess type = new BreakingBondReaction();
- Object[] params = {Boolean.TRUE};
- type.setParameters(params);
-
- /* initiate */
- IReactionSet setOfReactions = type.initiate(setOfReactants, null);
-
- Assert.assertEquals(2, setOfReactions.getReactionCount());
-
- // expected products
-
- //Smiles("C=[C+]")
- IMolecule expected1 = builder.newMolecule();
- expected1.addAtom(builder.newAtom("C"));
- expected1.addAtom(builder.newAtom("C"));
- expected1.getAtom(1).setFormalCharge(+1);
- expected1.addBond(0, 1, IBond.Order.DOUBLE);
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addAtom(builder.newAtom("H"));
- expected1.addBond(0, 2, IBond.Order.SINGLE);
- expected1.addBond(0, 3, IBond.Order.SINGLE);
- expected1.addBond(1, 4, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected1);
- IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
- IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected1);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product1,queryAtom));
-
- //Smiles("[C-]")
- IMolecule expected2 = builder.newMolecule();
- expected2.addAtom(builder.newAtom("C"));
- expected2.getAtom(0).setFormalCharge(-1);
- expected2.addAtom(builder.newAtom("H"));
- expected2.addAtom(builder.newAtom("H"));
- expected2.addAtom(builder.newAtom("H"));
- expected2.addBond(0, 1, IBond.Order.SINGLE);
- expected2.addBond(0, 2, IBond.Order.SINGLE);
- expected2.addBond(0, 3, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected2);
- lpcheck.saturate(expected2);
-
- IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected2);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product2,queryAtom));
-
- //Smiles("C=[C-]")
- expected1.getAtom(1).setFormalCharge(-1);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected1);
- lpcheck.saturate(expected1);
- product1 = setOfReactions.getReaction(1).getProducts().getMolecule(0);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected1);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product1,queryAtom));
-
- //Smiles("[C+]")
- expected2.getAtom(0).setFormalCharge(+1);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(expected2);
-
- product2 = setOfReactions.getReaction(1).getProducts().getMolecule(1);
- queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(expected2);
- Assert.assertTrue(UniversalIsomorphismTester.isIsomo...
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