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* $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
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* Copyright (C) 2006-2007 Miguel Rojas <miguel.rojas@uni-koeln.de>
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.reaction.type;
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import java.util.List;
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import org.openscience.cdk.CDKConstants;
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import org.openscience.cdk.DefaultChemObjectBuilder;
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import org.openscience.cdk.SingleElectron;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.graph.ConnectivityChecker;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IBond;
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import org.openscience.cdk.interfaces.IMapping;
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import org.openscience.cdk.interfaces.IMolecule;
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import org.openscience.cdk.interfaces.IMoleculeSet;
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import org.openscience.cdk.interfaces.IReaction;
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import org.openscience.cdk.interfaces.IReactionSet;
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import org.openscience.cdk.interfaces.ISingleElectron;
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import org.openscience.cdk.reaction.IReactionProcess;
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import org.openscience.cdk.reaction.ReactionSpecification;
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import org.openscience.cdk.tools.LoggingTool;
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* <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation.
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* This reaction could be represented as A-B-[c*] => [A*] + B=C.</p>
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* <p>Make sure that the molecule has the corresponend lone pair electrons
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* for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
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* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
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* setOfReactants.addMolecule(new Molecule());
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* IReactionProcess type = new RadicalSiteInitiationReaction();
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* Object[] params = {Boolean.FALSE};
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type.setParameters(params);
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* IReactionSet setOfReactions = type.initiate(setOfReactants, null);
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* <p>We have the possibility to localize the reactive center. Good method if you
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* want to localize the reaction in a fixed point</p>
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* <pre>atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);</pre>
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* <p>Moreover you must put the parameter Boolean.TRUE</p>
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* <p>If the reactive center is not localized then the reaction process will
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* try to find automatically the posible reactive center.</p>
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* @author Miguel Rojas
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* @cdk.created 2006-05-05
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* @cdk.module reaction
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* @cdk.set reaction-types
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public class RadicalSiteInitiationReaction implements IReactionProcess{
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private LoggingTool logger;
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private boolean hasActiveCenter;
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private static final int BONDTOFLAG = 8;
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* Constructor of the RadicalSiteInitiationReaction object
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public RadicalSiteInitiationReaction(){
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logger = new LoggingTool(this);
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* Gets the specification attribute of the RadicalSiteInitiationReaction object
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*@return The specification value
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public ReactionSpecification getSpecification() {
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return new ReactionSpecification(
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"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#RearrangementRadical3Reaction",
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this.getClass().getName(),
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"$Id: RadicalSiteInitiationReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
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"The Chemistry Development Kit");
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* Sets the parameters attribute of the RadicalSiteInitiationReaction object
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*@param params The parameter is if the molecule has already fixed the center active or not. It
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* should be set before to inize the reaction with a setFlag: CDKConstants.REACTIVE_CENTER
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*@exception CDKException Description of the Exception
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public void setParameters(Object[] params) throws CDKException {
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if (params.length > 1) {
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throw new CDKException("RadicalSiteInitiationReaction only expects one parameter");
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if (!(params[0] instanceof Boolean)) {
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throw new CDKException("The parameter 1 must be of type boolean");
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hasActiveCenter = ((Boolean) params[0]).booleanValue();
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* Gets the parameters attribute of the RadicalSiteInitiationReaction object
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*@return The parameters value
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public Object[] getParameters() {
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Object[] params = new Object[1];
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params[0] = new Boolean (hasActiveCenter);
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*@param reactants reactants of the reaction.
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*@param agents agents of the reaction (Must be in this case null).
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*@exception CDKException Description of the Exception
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public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
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logger.debug("initiate reaction: RadicalSiteInitiationReaction");
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if (reactants.getMoleculeCount() != 1) {
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throw new CDKException("RadicalSiteInitiationReaction only expects one reactant");
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if (agents != null) {
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throw new CDKException("RadicalSiteInitiationReaction don't expects agents");
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IReactionSet setOfReactions = reactants.getBuilder().newReactionSet();
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IMolecule reactant = reactants.getMolecule(0);
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/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
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if(!hasActiveCenter){
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setActiveCenters(reactant);
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IMolecule reactant0 = reactants.getMolecule(0);
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for(int i = 0 ; i < reactant0.getAtomCount() ; i++){
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atomi = reactant0.getAtom(i);
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if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)&& reactant.getConnectedSingleElectronsCount(atomi) == 1 ){
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java.util.List bonds = reactant.getConnectedBondsList(atomi);
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for(int j = 0 ; j < bonds.size() ; j++){
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bondj = (IBond)bonds.get(j);
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if(bondj.getFlag(CDKConstants.REACTIVE_CENTER)&& bondj.getOrder() < 3.0 ){
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IAtom atom = bondj.getConnectedAtom(reactant.getAtom(i));
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if(atom.getFormalCharge() != 0)
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java.util.List bondsI = reactant.getConnectedBondsList(atom);
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for(int k = 0 ; k < bondsI.size() ; k++){
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bondk = (IBond)bondsI.get(k);
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if(bondk.getFlag(CDKConstants.REACTIVE_CENTER) && bondk.getOrder() == 1.0 && !bondk.equals(bondj)){
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IAtom atomConn = bondk.getConnectedAtom(atom);
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if(atomConn.getFlag(CDKConstants.REACTIVE_CENTER) && atomConn.getFormalCharge() == 0
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&& !atomConn.equals(atomi) && !atomConn.getSymbol().equals("H")){
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IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
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reaction.addReactant(reactant);
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cleanFlagBOND(reactants.getMolecule(0));
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/* positions atoms and bonds */
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int atom0P = reactant.getAtomNumber(atomi);
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bondj.setFlag(BONDTOFLAG, true);
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int bond2P = reactant.getBondNumber(bondk);
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int atom1P = reactant.getAtomNumber(atom);
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int atom2P = reactant.getAtomNumber(atomConn);
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acCloned = (IMolecule) reactant.clone();
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} catch (CloneNotSupportedException e) {
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throw new CDKException("Could not clone IMolecule!", e);
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acCloned.removeBond(bond2P);
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List selectron = acCloned.getConnectedSingleElectronsList(acCloned.getAtom(atom0P));
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acCloned.removeSingleElectron((ISingleElectron)selectron.get(selectron.size() -1));
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selectron = acCloned.getConnectedSingleElectronsList(acCloned.getAtom(atom0P));
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acCloned.addSingleElectron(new SingleElectron(acCloned.getAtom(atom2P)));
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IBond bondjClon = null;
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for(int l = 0 ; l < acCloned.getBondCount();l++){
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if(acCloned.getBond(l).getFlag(BONDTOFLAG)){
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order = acCloned.getBond(l).getOrder();
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acCloned.getBond(l).setOrder(order+1);
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bondjClon = acCloned.getBond(l);
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IMapping mapping = atom.getBuilder().newMapping(atomi, acCloned.getAtom(atom0P));
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reaction.addMapping(mapping);
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mapping = atom.getBuilder().newMapping(atom, acCloned.getAtom(atom1P));
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reaction.addMapping(mapping);
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mapping = atom.getBuilder().newMapping(atomConn, acCloned.getAtom(atom2P));
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reaction.addMapping(mapping);
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mapping = atom.getBuilder().newMapping(bondj, bondjClon);
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reaction.addMapping(mapping);
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// mapping = atom.getBuilder().newMapping(bondk, acCloned.getBond(bond2P));
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// reaction.addMapping(mapping);
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IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(acCloned);
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for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){
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reaction.addProduct(moleculeSet.getMolecule(z));
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setOfReactions.addReaction(reaction);
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bondj.setFlag(BONDTOFLAG, false);
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return setOfReactions;
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* set the active center for this molecule.
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* The active center will be those which correspond with A-B-[C*].
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* C: Atom with single electron
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* @param reactant The molecule to set the activity
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* @throws CDKException
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private void setActiveCenters(IMolecule reactant) throws CDKException {
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for(int i = 0 ; i < reactant.getAtomCount() ; i++) {
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atomi = reactant.getAtom(i);
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if(reactant.getConnectedSingleElectronsCount(atomi) == 1 ){
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java.util.List bonds = reactant.getConnectedBondsList(atomi);
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for(int j = 0 ; j < bonds.size() ; j++){
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bondj = (IBond)bonds.get(j);
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if(bondj.getOrder() < 3.0){
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IAtom atom = bondj.getConnectedAtom(atomi);
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if(atom.getFormalCharge() != 0)
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java.util.List bondsI = reactant.getConnectedBondsList(atom);
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for(int k = 0 ; k < bondsI.size() ; k++){
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bondk = (IBond)bondsI.get(k);
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if(bondk.getOrder() == 1 && !bondk.equals(bondj)){
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IAtom atomConn = bondk.getConnectedAtom(atom);
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if(atomConn.getFormalCharge() == 0 && !atomConn.getSymbol().equals("H")){
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atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
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atom.setFlag(CDKConstants.REACTIVE_CENTER,true);
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atomConn.setFlag(CDKConstants.REACTIVE_CENTER,true);
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bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
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bondk.setFlag(CDKConstants.REACTIVE_CENTER,true);
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* Gets the parameterNames attribute of the RadicalSiteInitiationReaction object
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*@return The parameterNames value
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public String[] getParameterNames() {
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String[] params = new String[1];
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params[0] = "hasActiveCenter";
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* Gets the parameterType attribute of the RadicalSiteInitiationReaction object
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*@param name Description of the Parameter
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*@return The parameterType value
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public Object getParameterType(String name) {
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return new Boolean(false);
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* clean the flags BONDTOFLAG from the molecule
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public void cleanFlagBOND(IAtomContainer ac){
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for(int j = 0 ; j < ac.getBondCount(); j++)
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ac.getBond(j).setFlag(BONDTOFLAG, false);
added
removed
src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
