/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2008 Miguel Rojas <miguelrojasch@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionEngine;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* <p>IReactionProcess which participate in movement resonance.
* This reaction could be represented as [A-]-B=C => A=B-[C-]. Due to
* excess of charge of the atom B, the double bond in the position 2 is
* desplaced.</p>
* <p>Make sure that the molecule has the correspond lone pair electrons
* for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
* <p>It is processed by the RearrangementChargeMechanism class</p>
*
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
* IReactionProcess type = new RearrangementAnionReaction();
* 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 localize 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 localized then the reaction process will
* try to find automatically the possible reactive center.</p>
*
*
* @author Miguel Rojas
*
* @cdk.created 2006-05-05
* @cdk.module reaction
* @cdk.githash
* @cdk.set reaction-types
*
* @see RearrangementChargeMechanism
**/
@TestClass(value="org.openscience.cdk.reaction.type.RearrangementAnionReactionTest")
public class RearrangementAnionReaction extends ReactionEngine implements IReactionProcess{
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(RearrangementAnionReaction.class);
/**
* Constructor of the RearrangementAnionReaction object
*
*/
public RearrangementAnionReaction(){
}
/**
* Gets the specification attribute of the RearrangementAnionReaction object
*
*@return The specification value
*/
@TestMethod("testGetSpecification")
public ReactionSpecification getSpecification() {
return new ReactionSpecification(
"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#RearrangementAnion",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* 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
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
logger.debug("initiate reaction: RearrangementAnionReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("RearrangementAnionReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("RearrangementAnionReaction 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*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if( ipr != null && !ipr.isSetParameter())
setActiveCenters(reactant);
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)&& atomi.getFormalCharge() == -1 &&
reactant.getConnectedLonePairsCount(atomi) > 0){
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while(bondis.hasNext()){
IBond bondi = bondis.next();
if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)&& bondi.getOrder() == IBond.Order.SINGLE){
IAtom atomj = bondi.getConnectedAtom(atomi);
if(atomj.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atomj) == 0){
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
while(bondjs.hasNext()){
IBond bondj = bondjs.next();
if(bondj.equals(bondi))
continue;
if(bondj.getFlag(CDKConstants.REACTIVE_CENTER) && bondj.getOrder() == IBond.Order.DOUBLE ){
IAtom atomk = bondj.getConnectedAtom(atomj);
if(atomk.getFlag(CDKConstants.REACTIVE_CENTER)&&
reactant.getConnectedSingleElectronsCount(atomk) == 0 &&
(atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge()) >= 0){
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
atomList.add(atomi);
atomList.add(atomj);
atomList.add(atomk);
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
bondList.add(bondj);
IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if(reaction == null)
continue;
else
setOfReactions.addReaction(reaction);
}
}
}
}
}
}
}
}
return setOfReactions;
}
/**
* set the active center for this molecule.
* The active center will be those which correspond with [A-]-B=C.
* <pre>
* A: Atom with negative charge (Moreover it contains lone pair electrons)
* -: Single bond
* B: Atom
* =: Double bond
* C: Atom
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
if(atomi.getFormalCharge() == -1 && reactant.getConnectedLonePairsCount(atomi) > 0 ){
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while(bondis.hasNext()){
IBond bondi = bondis.next();
if(bondi.getOrder() == IBond.Order.SINGLE){
IAtom atomj = bondi.getConnectedAtom(atomi);
if((atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atomj) == 0){
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
while(bondjs.hasNext()){
IBond bondj = bondjs.next();
if(bondj.equals(bondi))
continue;
if(bondj.getOrder() == IBond.Order.DOUBLE ){
IAtom atomk = bondj.getConnectedAtom(atomj);
if(reactant.getConnectedSingleElectronsCount(atomk) == 0 &&
(atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge()) >= 0){
atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
atomj.setFlag(CDKConstants.REACTIVE_CENTER,true);
atomk.setFlag(CDKConstants.REACTIVE_CENTER,true);
bondi.setFlag(CDKConstants.REACTIVE_CENTER,true);
bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
}
}
}
}
}
}
}
}
}
}