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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.exception.CDKException;
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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.ILonePair;
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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.IRingSet;
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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.ringsearch.AllRingsFinder;
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import org.openscience.cdk.tools.LoggingTool;
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import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
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* <p>IReactionProcess which participate in movement resonance.
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* This reaction could be represented as [A+]-B| => A=[B+]. Due to
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* deficiency of charge of the atom A, the lone pair electron of the atom A is
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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 RearrangementCation1Reaction();
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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 RearrangementCation1Reaction implements IReactionProcess{
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private LoggingTool logger;
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private boolean hasActiveCenter;
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private static final int BONDTOFLAG1 = 8;
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* Constructor of the RearrangementCation1Reaction object
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public RearrangementCation1Reaction(){
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logger = new LoggingTool(this);
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* Gets the specification attribute of the RearrangementCation1Reaction 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#RearrangementCation1Reaction",
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this.getClass().getName(),
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"$Id: RearrangementCation1Reaction.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 RearrangementCation1Reaction 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("RearrangementCation1Reaction 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 RearrangementCation1Reaction 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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* It is needed to call the addExplicitHydrogensToSatisfyValency
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* from the class tools.HydrogenAdder.
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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: RearrangementCation1Reaction");
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if (reactants.getMoleculeCount() != 1) {
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throw new CDKException("RearrangementCation1Reaction only expects one reactant");
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if (agents != null) {
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throw new CDKException("RearrangementCation1Reaction don't expects agents");
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IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().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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/*control of the volume of number of charge - it will be made possible if
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* if the atoms[i] is the only atom with charge*/
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int negCharge = AtomContainerManipulator.getTotalNegativeFormalCharge((IAtomContainer)reactant);
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int posCharge = AtomContainerManipulator.getTotalPositiveFormalCharge((IAtomContainer)reactant);
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if(posCharge > 1 || Math.abs(negCharge) > 1)
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return setOfReactions;
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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(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getFormalCharge() == 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() == 1.0){
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IAtom atom1 = bondj.getConnectedAtom(atomi);
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List lp = reactant.getConnectedLonePairsList(atom1);
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if(atom1.getFlag(CDKConstants.REACTIVE_CENTER) && lp.size() > 0 )
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if(reactant.getConnectedSingleElectronsCount(atom1) == 0){
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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(BONDTOFLAG1, true);
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int atom1P = reactant.getAtomNumber(atom1);
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IAtomContainer acCloned;
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acCloned = (IAtomContainer)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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int charge = acCloned.getAtom(atom0P).getFormalCharge();
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acCloned.getAtom(atom0P).setFormalCharge(charge-1);
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IBond bondjClon = null;
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for(int l = 0 ; l<acCloned.getBondCount();l++){
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IBond bb = acCloned.getBond(l);
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if(bb.getFlag(BONDTOFLAG1)){
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double order = bb.getOrder();
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bb.setOrder(order+1);
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charge = acCloned.getAtom(atom1P).getFormalCharge();
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acCloned.getAtom(atom1P).setFormalCharge(charge+1);
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List selectron = acCloned.getConnectedLonePairsList(acCloned.getAtom(atom1P));
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acCloned.removeLonePair((ILonePair)selectron.get(selectron.size() -1));
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IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomi, acCloned.getAtom(atom0P));
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reaction.addMapping(mapping);
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mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom1, acCloned.getAtom(atom1P));
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reaction.addMapping(mapping);
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mapping = DefaultChemObjectBuilder.getInstance().newMapping(bondj, bondjClon);
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reaction.addMapping(mapping);
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reaction.addProduct((IMolecule) acCloned);
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setOfReactions.addReaction(reaction);
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bondj.setFlag(BONDTOFLAG1, 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|.
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* A: Atom with positive charge
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* B: Atom with lone pair electrons
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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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AllRingsFinder ssrF = new AllRingsFinder();
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IRingSet rings = ssrF.findAllRings(reactant);
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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(atomi.getFormalCharge() == 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() == 1.0){
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IAtom atom = bondj.getConnectedAtom(atomi);
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List lp = reactant.getConnectedLonePairsList(atom);
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if((lp.size() > 0 )&& (atom.getFormalCharge() == 0))
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if(reactant.getConnectedSingleElectronsCount(atom) == 0){
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if(rings.contains(atom))
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atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
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atom.setFlag(CDKConstants.REACTIVE_CENTER,true);
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bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
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* Gets the parameterNames attribute of the RearrangementCation1Reaction 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 RearrangementCation1Reaction 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(BONDTOFLAG1, false);
added
removed
src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java
