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[Cdk-commits] SF.net SVN: cdk: [10090] branches/miguelrojasch/reaction/src/org/ openscience/cdk
|
From: <mig...@us...> - 2008-02-13 20:25:41
|
Revision: 10090
http://cdk.svn.sourceforge.net/cdk/?rev=10090&view=rev
Author: miguelrojasch
Date: 2008-02-13 12:25:20 -0800 (Wed, 13 Feb 2008)
Log Message:
-----------
changed the name of Adduction to AdductionLP which specifies more specific according to adduction from LonePair orbitals.
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionProtonReactionTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionSodiumReactionTest.java
Added Paths:
-----------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java
Removed Paths:
-------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionMechanism.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonReaction.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumReaction.java
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java (from rev 10089, branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionMechanism.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -0,0 +1,135 @@
+/* $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.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.ILonePair;
+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;
+
+/**
+ * <p>This mechanism adduct together two fragments. The second fragment will be deficient in charge.
+ * It returns the reaction mechanism which has been cloned the IMolecule.</p>
+ * <p>This reaction could be represented as A + [B+] => A-B</p>
+ *
+ *
+ * @author miguelrojasch
+ * @cdk.created 2008-02-10
+ * @cdk.module reaction
+ *
+ */
+public class AdductionLPMechanism implements IReactionMechanism{
+
+ private CDKAtomTypeMatcher atMatcher;
+
+ /**
+ * Constructor of the AdductionLPMechanism object.
+ *
+ */
+ public AdductionLPMechanism(){
+ atMatcher = CDKAtomTypeMatcher.getInstance(
+ NoNotificationChemObjectBuilder.getInstance(),
+ CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
+ );
+ }
+
+ /**
+ * Initiates the process for the given mechanism. The atoms and bonds 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.
+ * @param bondList The list of bonds taking part in the mechanism. not allowed bonds.
+ *
+ * @return The Reaction mechanism
+ *
+ */
+ public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
+ if (moleculeSet.getMoleculeCount() != 2) {
+ throw new CDKException("TautomerizationMechanism expects two IMolecule's");
+ }
+ if (atomList.size() != 2) {
+ throw new CDKException("TautomerizationMechanism expects two atoms in the ArrayList");
+ }
+ if (bondList != null) {
+ throw new CDKException("TautomerizationMechanism don't expect bonds in the ArrayList");
+ }
+ IMolecule molecule = moleculeSet.getMolecule(0);
+ IMolecule reactantCloned;
+ try {
+ reactantCloned = (IMolecule) moleculeSet.getMolecule(0).clone();
+ reactantCloned.add((IAtomContainer) moleculeSet.getMolecule(1).clone());
+ } catch (CloneNotSupportedException e) {
+ throw new CDKException("Could not clone IMolecule!", e);
+ }
+ IAtom atom1 = atomList.get(0);// Atom 1: excess in charge
+ int posAtom1 = moleculeSet.getMolecule(0).getAtomNumber(atom1);
+ IAtom atom2 = atomList.get(1);// Atom 2: deficient in charge
+ int posAtom2 = moleculeSet.getMolecule(1).getAtomNumber(atom2)+moleculeSet.getMolecule(0).getAtomCount();
+
+ IBond newBond = molecule.getBuilder().newBond(reactantCloned.getAtom(posAtom1), reactantCloned.getAtom(posAtom2), IBond.Order.SINGLE);
+ reactantCloned.addBond(newBond);
+
+ int charge = reactantCloned.getAtom(posAtom1).getFormalCharge();
+ reactantCloned.getAtom(posAtom1).setFormalCharge(charge+1);
+ List<ILonePair> lps = reactantCloned.getConnectedLonePairsList(reactantCloned.getAtom(posAtom1));
+ reactantCloned.removeLonePair(lps.get(lps.size() - 1));
+ 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.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);
+
+ reaction.addProduct(reactantCloned);
+
+ return reaction;
+ }
+
+}
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionMechanism.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionMechanism.java 2008-02-13 20:03:59 UTC (rev 10089)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/AdductionMechanism.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -1,135 +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 java.util.List;
-
-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.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.ILonePair;
-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;
-
-/**
- * <p>This mechanism adduct together two fragments. The second fragment will be deficient in charge.
- * It returns the reaction mechanism which has been cloned the IMolecule.</p>
- * <p>This reaction could be represented as A + [B+] => A-B</p>
- *
- *
- * @author miguelrojasch
- * @cdk.created 2008-02-10
- * @cdk.module reaction
- *
- */
-public class AdductionMechanism implements IReactionMechanism{
-
- private CDKAtomTypeMatcher atMatcher;
-
- /**
- * Constructor of the AdductionMechanism object.
- *
- */
- public AdductionMechanism(){
- atMatcher = CDKAtomTypeMatcher.getInstance(
- NoNotificationChemObjectBuilder.getInstance(),
- CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
- );
- }
-
- /**
- * Initiates the process for the given mechanism. The atoms and bonds 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.
- * @param bondList The list of bonds taking part in the mechanism. not allowed bonds.
- *
- * @return The Reaction mechanism
- *
- */
- public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
- if (moleculeSet.getMoleculeCount() != 2) {
- throw new CDKException("TautomerizationMechanism expects two IMolecule's");
- }
- if (atomList.size() != 2) {
- throw new CDKException("TautomerizationMechanism expects two atoms in the ArrayList");
- }
- if (bondList != null) {
- throw new CDKException("TautomerizationMechanism don't expect bonds in the ArrayList");
- }
- IMolecule molecule = moleculeSet.getMolecule(0);
- IMolecule reactantCloned;
- try {
- reactantCloned = (IMolecule) moleculeSet.getMolecule(0).clone();
- reactantCloned.add((IAtomContainer) moleculeSet.getMolecule(1).clone());
- } catch (CloneNotSupportedException e) {
- throw new CDKException("Could not clone IMolecule!", e);
- }
- IAtom atom1 = atomList.get(0);// Atom 1: excess in charge
- int posAtom1 = moleculeSet.getMolecule(0).getAtomNumber(atom1);
- IAtom atom2 = atomList.get(1);// Atom 2: deficient in charge
- int posAtom2 = moleculeSet.getMolecule(1).getAtomNumber(atom2)+moleculeSet.getMolecule(0).getAtomCount();
-
- IBond newBond = molecule.getBuilder().newBond(reactantCloned.getAtom(posAtom1), reactantCloned.getAtom(posAtom2), IBond.Order.SINGLE);
- reactantCloned.addBond(newBond);
-
- int charge = reactantCloned.getAtom(posAtom1).getFormalCharge();
- reactantCloned.getAtom(posAtom1).setFormalCharge(charge+1);
- List<ILonePair> lps = reactantCloned.getConnectedLonePairsList(reactantCloned.getAtom(posAtom1));
- reactantCloned.removeLonePair(lps.get(lps.size() - 1));
- 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.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);
-
- reaction.addProduct(reactantCloned);
-
- return reaction;
- }
-
-}
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java (from rev 10088, branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonReaction.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -0,0 +1,236 @@
+/*
+ * $RCSfile$
+ * $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.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.AdductionLPMechanism;
+import org.openscience.cdk.tools.LoggingTool;
+
+/**
+ * <p>IReactionProcess which produces a protonation.
+ * As most commonly encountered, this reaction results in the formal migration
+ * of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond</p>
+ *
+ * <pre>[X-] + [H+] => X -H</pre>
+ * <pre>|X + [H+] => [X+]-H</pre>
+ *
+ * <p>Below you have an example how to initiate the mechanism.</p>
+ * <p>It is processed by the AdductionLPMechanism class</p>
+ * <pre>
+ * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ * setOfReactants.addMolecule(new Molecule());
+ * IReactionProcess type = new AdductionProtonLPReaction();
+ * 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 2008-02-11
+ * @cdk.module reaction
+ * @cdk.set reaction-types
+ *
+ * @see AdductionLPMechanism
+ **/
+public class AdductionProtonLPReaction implements IReactionProcess{
+ private LoggingTool logger;
+ private boolean hasActiveCenter;
+ private IReactionMechanism mechanism;
+
+ /**
+ * Constructor of the AdductionProtonLPReaction object.
+ *
+ */
+ public AdductionProtonLPReaction(){
+ logger = new LoggingTool(this);
+ mechanism = new AdductionLPMechanism();
+ }
+
+ /**
+ * Gets the specification attribute of the AdductionProtonLPReaction object.
+ *
+ *@return The specification value
+ */
+ public ReactionSpecification getSpecification() {
+ return new ReactionSpecification(
+ "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#ProtonationReaction",
+ this.getClass().getName(),
+ "$Id: AdductionProtonLPReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
+ "The Chemistry Development Kit");
+ }
+
+ /**
+ * Sets the parameters attribute of the AdductionProtonLPReaction 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("AdductionProtonLPReaction 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 AdductionProtonLPReaction 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: AdductionProtonLPReaction");
+
+ if (reactants.getMoleculeCount() != 1) {
+ throw new CDKException("AdductionProtonLPReaction only expects one reactant");
+ }
+ if (agents != null) {
+ throw new CDKException("AdductionProtonLPReaction 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<IAtom> atoms = reactant.atoms();
+ while (atoms.hasNext()) {
+ IAtom atomi = atoms.next(); // Atom pos 1
+ if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() <= 0
+ && reactant.getConnectedLonePairsCount(atomi) > 0 && reactant.getConnectedSingleElectronsCount(atomi) > 0){
+
+ ArrayList<IAtom> atomList = new ArrayList<IAtom>();
+ atomList.add(atomi);
+ IAtom atomH = reactant.getBuilder().newAtom("H");
+ atomH.setFormalCharge(1);
+ atomList.add(atomH);
+
+ IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
+ moleculeSet.addMolecule(reactant);
+ IMolecule adduct = reactant.getBuilder().newMolecule();
+ adduct.addAtom(atomH);
+ moleculeSet.addMolecule(adduct);
+
+ IReaction reaction = mechanism.initiate(moleculeSet, atomList, null);
+ 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 X=Y-Z-H.
+ * <pre>
+ * [X-]
+ * </pre>
+ *
+ * @param reactant The molecule to set the activity
+ * @throws CDKException
+ */
+ private void setActiveCenters(IMolecule reactant) throws CDKException {
+ Iterator<IAtom> atoms = reactant.atoms();
+ while (atoms.hasNext()) {
+ IAtom atomi = atoms.next(); // Atom pos 1
+ if(atomi.getFormalCharge() <= 0 && reactant.getConnectedLonePairsCount(atomi) > 0
+ && reactant.getConnectedSingleElectronsCount(atomi) > 0){
+ atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
+
+ }
+ }
+ }
+ /**
+ * Gets the parameterNames attribute of the AdductionProtonLPReaction object.
+ *
+ *@return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ String[] params = new String[1];
+ params[0] = "hasActiveCenter";
+ return params;
+ }
+
+
+ /**
+ * Gets the parameterType attribute of the AdductionProtonLPReaction object.
+ *
+ *@param name Description of the Parameter
+ *@return The parameterType value
+ */
+ public Object getParameterType(String name) {
+ return new Boolean(false);
+ }
+}
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonReaction.java 2008-02-13 20:03:59 UTC (rev 10089)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionProtonReaction.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -1,235 +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.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.AdductionMechanism;
-import org.openscience.cdk.tools.LoggingTool;
-
-/**
- * <p>IReactionProcess which produces a protonation.
- * As most commonly encountered, this reaction results in the formal migration
- * of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond</p>
- *
- * <pre>[X-] + [H+] => X -H</pre>
- * <pre>|X + [H+] => [X+]-H</pre>
- *
- * <p>Below you have an example how to initiate the mechanism.</p>
- * <p>It is processed by the AdductionMechanism class</p>
- * <pre>
- * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
- * setOfReactants.addMolecule(new Molecule());
- * IReactionProcess type = new AdductionProtonReaction();
- * 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 2008-02-11
- * @cdk.module reaction
- * @cdk.set reaction-types
- *
- * @see AdductionMechanism
- **/
-public class AdductionProtonReaction implements IReactionProcess{
- private LoggingTool logger;
- private boolean hasActiveCenter;
- private IReactionMechanism mechanism;
-
- /**
- * Constructor of the AdductionProtonReaction object.
- *
- */
- public AdductionProtonReaction(){
- logger = new LoggingTool(this);
- mechanism = new AdductionMechanism();
- }
-
- /**
- * Gets the specification attribute of the AdductionProtonReaction object.
- *
- *@return The specification value
- */
- public ReactionSpecification getSpecification() {
- return new ReactionSpecification(
- "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#ProtonationReaction",
- this.getClass().getName(),
- "$Id: AdductionProtonReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
- "The Chemistry Development Kit");
- }
-
- /**
- * Sets the parameters attribute of the AdductionProtonReaction 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("AdductionProtonReaction 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 AdductionProtonReaction 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: AdductionProtonReaction");
-
- if (reactants.getMoleculeCount() != 1) {
- throw new CDKException("AdductionProtonReaction only expects one reactant");
- }
- if (agents != null) {
- throw new CDKException("AdductionProtonReaction 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<IAtom> atoms = reactant.atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next(); // Atom pos 1
- if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() <= 0
- && reactant.getConnectedLonePairsCount(atomi) > 0){
-
- ArrayList<IAtom> atomList = new ArrayList<IAtom>();
- atomList.add(atomi);
- IAtom atomH = reactant.getBuilder().newAtom("H");
- atomH.setFormalCharge(1);
- atomList.add(atomH);
-
- IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
- moleculeSet.addMolecule(reactant);
- IMolecule adduct = reactant.getBuilder().newMolecule();
- adduct.addAtom(atomH);
- moleculeSet.addMolecule(adduct);
-
- IReaction reaction = mechanism.initiate(moleculeSet, atomList, null);
- 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 X=Y-Z-H.
- * <pre>
- * [X-]
- * </pre>
- *
- * @param reactant The molecule to set the activity
- * @throws CDKException
- */
- private void setActiveCenters(IMolecule reactant) throws CDKException {
- Iterator<IAtom> atoms = reactant.atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next(); // Atom pos 1
- if(atomi.getFormalCharge() <= 0 && reactant.getConnectedLonePairsCount(atomi) > 0){
- atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
-
- }
- }
- }
- /**
- * Gets the parameterNames attribute of the AdductionProtonReaction object.
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "hasActiveCenter";
- return params;
- }
-
-
- /**
- * Gets the parameterType attribute of the AdductionProtonReaction object.
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- return new Boolean(false);
- }
-}
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java (from rev 10088, branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumReaction.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -0,0 +1,236 @@
+/*
+ * $RCSfile$
+ * $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.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.AdductionLPMechanism;
+import org.openscience.cdk.tools.LoggingTool;
+
+/**
+ * <p>IReactionProcess which produces an adduction of the Sodium.
+ * As most commonly encountered, this reaction results in the formal migration
+ * of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond</p>
+ *
+ * <pre>[X-] + [Na+] => X -Na</pre>
+ * <pre>|X + [Na+] => [X+]-Na</pre>
+ *
+ * <p>Below you have an example how to initiate the mechanism.</p>
+ * <p>It is processed by the AdductionLPMechanism class</p>
+ * <pre>
+ * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ * setOfReactants.addMolecule(new Molecule());
+ * IReactionProcess type = new AdductionSodiumLPReaction();
+ * 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 2008-02-11
+ * @cdk.module reaction
+ * @cdk.set reaction-types
+ *
+ * @see AdductionLPMechanism
+ **/
+public class AdductionSodiumLPReaction implements IReactionProcess{
+ private LoggingTool logger;
+ private boolean hasActiveCenter;
+ private IReactionMechanism mechanism;
+
+ /**
+ * Constructor of the AdductionSodiumLPReaction object.
+ *
+ */
+ public AdductionSodiumLPReaction(){
+ logger = new LoggingTool(this);
+ mechanism = new AdductionLPMechanism();
+ }
+
+ /**
+ * Gets the specification attribute of the AdductionSodiumLPReaction object.
+ *
+ *@return The specification value
+ */
+ public ReactionSpecification getSpecification() {
+ return new ReactionSpecification(
+ "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#ProtonationReaction",
+ this.getClass().getName(),
+ "$Id: AdductionSodiumLPReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
+ "The Chemistry Development Kit");
+ }
+
+ /**
+ * Sets the parameters attribute of the AdductionSodiumLPReaction 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("AdductionSodiumLPReaction 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 AdductionSodiumLPReaction 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: AdductionSodiumLPReaction");
+
+ if (reactants.getMoleculeCount() != 1) {
+ throw new CDKException("AdductionSodiumLPReaction only expects one reactant");
+ }
+ if (agents != null) {
+ throw new CDKException("AdductionSodiumLPReaction 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<IAtom> atoms = reactant.atoms();
+ while (atoms.hasNext()) {
+ IAtom atomi = atoms.next(); // Atom pos 1
+ if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() <= 0
+ && reactant.getConnectedLonePairsCount(atomi) > 0 && reactant.getConnectedSingleElectronsCount(atomi) > 0){
+
+ ArrayList<IAtom> atomList = new ArrayList<IAtom>();
+ atomList.add(atomi);
+ IAtom atomH = reactant.getBuilder().newAtom("Na");
+ atomH.setFormalCharge(1);
+ atomList.add(atomH);
+
+ IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
+ moleculeSet.addMolecule(reactant);
+ IMolecule adduct = reactant.getBuilder().newMolecule();
+ adduct.addAtom(atomH);
+ moleculeSet.addMolecule(adduct);
+
+ IReaction reaction = mechanism.initiate(moleculeSet, atomList, null);
+ 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 X=Y-Z-Na.
+ * <pre>
+ * [X-]
+ * </pre>
+ *
+ * @param reactant The molecule to set the activity
+ * @throws CDKException
+ */
+ private void setActiveCenters(IMolecule reactant) throws CDKException {
+ Iterator<IAtom> atoms = reactant.atoms();
+ while (atoms.hasNext()) {
+ IAtom atomi = atoms.next(); // Atom pos 1
+ if(atomi.getFormalCharge() <= 0 && reactant.getConnectedLonePairsCount(atomi) > 0
+ && reactant.getConnectedSingleElectronsCount(atomi) > 0){
+ atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
+
+ }
+ }
+ }
+ /**
+ * Gets the parameterNames attribute of the AdductionSodiumLPReaction object.
+ *
+ *@return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ String[] params = new String[1];
+ params[0] = "hasActiveCenter";
+ return params;
+ }
+
+
+ /**
+ * Gets the parameterType attribute of the AdductionSodiumLPReaction object.
+ *
+ *@param name Description of the Parameter
+ *@return The parameterType value
+ */
+ public Object getParameterType(String name) {
+ return new Boolean(false);
+ }
+}
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumReaction.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumReaction.java 2008-02-13 20:03:59 UTC (rev 10089)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/AdductionSodiumReaction.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -1,235 +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.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.AdductionMechanism;
-import org.openscience.cdk.tools.LoggingTool;
-
-/**
- * <p>IReactionProcess which produces an adduction of the Sodium.
- * As most commonly encountered, this reaction results in the formal migration
- * of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond</p>
- *
- * <pre>[X-] + [Na+] => X -Na</pre>
- * <pre>|X + [Na+] => [X+]-Na</pre>
- *
- * <p>Below you have an example how to initiate the mechanism.</p>
- * <p>It is processed by the AdductionMechanism class</p>
- * <pre>
- * IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
- * setOfReactants.addMolecule(new Molecule());
- * IReactionProcess type = new AdductionSodiumReaction();
- * 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 2008-02-11
- * @cdk.module reaction
- * @cdk.set reaction-types
- *
- * @see AdductionMechanism
- **/
-public class AdductionSodiumReaction implements IReactionProcess{
- private LoggingTool logger;
- private boolean hasActiveCenter;
- private IReactionMechanism mechanism;
-
- /**
- * Constructor of the AdductionSodiumReaction object.
- *
- */
- public AdductionSodiumReaction(){
- logger = new LoggingTool(this);
- mechanism = new AdductionMechanism();
- }
-
- /**
- * Gets the specification attribute of the AdductionSodiumReaction object.
- *
- *@return The specification value
- */
- public ReactionSpecification getSpecification() {
- return new ReactionSpecification(
- "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#ProtonationReaction",
- this.getClass().getName(),
- "$Id: AdductionSodiumReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
- "The Chemistry Development Kit");
- }
-
- /**
- * Sets the parameters attribute of the AdductionSodiumReaction 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("AdductionSodiumReaction 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 AdductionSodiumReaction 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: AdductionSodiumReaction");
-
- if (reactants.getMoleculeCount() != 1) {
- throw new CDKException("AdductionSodiumReaction only expects one reactant");
- }
- if (agents != null) {
- throw new CDKException("AdductionSodiumReaction 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<IAtom> atoms = reactant.atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next(); // Atom pos 1
- if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() <= 0
- && reactant.getConnectedLonePairsCount(atomi) > 0){
-
- ArrayList<IAtom> atomList = new ArrayList<IAtom>();
- atomList.add(atomi);
- IAtom atomH = reactant.getBuilder().newAtom("Na");
- atomH.setFormalCharge(1);
- atomList.add(atomH);
-
- IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
- moleculeSet.addMolecule(reactant);
- IMolecule adduct = reactant.getBuilder().newMolecule();
- adduct.addAtom(atomH);
- moleculeSet.addMolecule(adduct);
-
- IReaction reaction = mechanism.initiate(moleculeSet, atomList, null);
- 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 X=Y-Z-Na.
- * <pre>
- * [X-]
- * </pre>
- *
- * @param reactant The molecule to set the activity
- * @throws CDKException
- */
- private void setActiveCenters(IMolecule reactant) throws CDKException {
- Iterator<IAtom> atoms = reactant.atoms();
- while (atoms.hasNext()) {
- IAtom atomi = atoms.next(); // Atom pos 1
- if(atomi.getFormalCharge() <= 0 && reactant.getConnectedLonePairsCount(atomi) > 0){
- atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
-
- }
- }
- }
- /**
- * Gets the parameterNames attribute of the AdductionSodiumReaction object.
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "hasActiveCenter";
- return params;
- }
-
-
- /**
- * Gets the parameterType attribute of the AdductionSodiumReaction 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/test/reaction/type/AdductionProtonReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionProtonReactionTest.java 2008-02-13 20:03:59 UTC (rev 10089)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionProtonReactionTest.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -41,7 +41,7 @@
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.AdductionProtonReaction;
+import org.openscience.cdk.reaction.type.AdductionProtonLPReaction;
import org.openscience.cdk.test.reaction.ReactionProcessTest;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -61,7 +61,7 @@
* The JUnit setup method
*/
@BeforeClass public static void setUp() throws Exception {
- setReaction(AdductionProtonReaction.class);
+ setReaction(AdductionProtonLPReaction.class);
}
/**
@@ -75,7 +75,7 @@
*/
@Test public void testAutomaticCentreActive() throws Exception {
- IReactionProcess type = new AdductionProtonReaction();
+ IReactionProcess type = new AdductionProtonLPReaction();
IMolecule molecule = getAcetaldehyde();
@@ -108,7 +108,7 @@
* @return The test suite
*/
@Test public void testManuallyCentreActive() throws Exception {
- IReactionProcess type = new AdductionProtonReaction();
+ IReactionProcess type = new AdductionProtonLPReaction();
IMolecule molecule = getAcetaldehyde();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -140,7 +140,7 @@
* @return The test suite
*/
@Test public void testCentreActive() throws Exception {
- IReactionProcess type = new AdductionProtonReaction();
+ IReactionProcess type = new AdductionProtonLPReaction();
Object[] object = type.getParameters();
Assert.assertFalse(((Boolean) object[0]).booleanValue());
@@ -158,7 +158,7 @@
* @return The test suite
*/
@Test public void testCDKConstants_REACTIVE_CENTER() throws Exception {
- IReactionProcess type = new AdductionProtonReaction();
+ IReactionProcess type = new AdductionProtonLPReaction();
IMoleculeSet setOfReactants = builder.newMoleculeSet();
IMolecule molecule = getAcetaldehyde();
@@ -203,7 +203,7 @@
* @return The test suite
*/
@Test public void testMapping() throws Exception {
- IReactionProcess type = new AdductionProtonReaction();
+ IReactionProcess type = new AdductionProtonLPReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
IMolecule molecule = getAcetaldehyde();
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionSodiumReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionSodiumReactionTest.java 2008-02-13 20:03:59 UTC (rev 10089)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/AdductionSodiumReactionTest.java 2008-02-13 20:25:20 UTC (rev 10090)
@@ -41,7 +41,7 @@
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.AdductionSodiumReaction;
+import org.openscience.cdk.reaction.type.AdductionSodiumLPReaction;
import org.openscience.cdk.test.reaction.ReactionProcessTest;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -61,7 +61,7 @@
* The JUnit setup method
*/
@BeforeClass public static void setUp() throws Exception {
- setReaction(AdductionSodiumReaction.class);
+ setReaction(AdductionSodiumLPReaction.class);
}
/**
@@ -75,7 +75,7 @@
*/
@Test public void testAutomaticCentreActive() throws Exception {
- IReactionProcess type = new AdductionSodiumReaction();
+ IReactionProcess type = new AdductionSodiumLPReaction();
IMolecule molecule = getAcetaldehyde();
@@ -108,7 +108,7 @@
* @return The test suite
*/
@Test public void testManuallyCentreActive() throws Exception {
- IReactionProcess type = new AdductionSodiumReaction();
+ IReactionProcess type = new AdductionSodiumLPReaction();
IMolecule molecule = getAcetaldehyde();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -140,7 +140,7 @@
* @return The test suite
*/
@Test public void testCentreActive() throws Exception {
- IReactionProcess type = new AdductionSodiumReaction();
+ IReactionProcess type = new AdductionSodiumLPReaction();
Object[] object = type.getParameters();
Assert.assertFalse(((Boolean) object[0]).booleanValue());
@@ -158,7 +158,7 @@
* @return The test suite
*/
@Test public void testCDKConstants_REACTIVE_CENTER() throws Exception {
- IReactionProcess type = new AdductionSodiumReaction();
+ IReactionProcess type = new AdductionSodiumLPReaction();
IMoleculeSet setOfReactants = builder.newMoleculeSet();
IMolecule molecule = getAcetaldehyde();
@@ -203,7 +203,7 @@
* @return The test suite
*/
@Test public void testMapping() throws Exception {
- IReactionProcess type = new AdductionSodiumReaction();
+ IReactionProcess type = new AdductionSodiumLPReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
IMolecule molecule = getAcetaldehyde();
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