/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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 java.util.List;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
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.interfaces.IRingSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionEngine;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.HOSECodeGenerator;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* <p>
* This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*]. Due to
* the single electron of atom A the R is moved.</p>
* <p>It is processed by the RadicalSiteRearrangementMechanism class</p>
*
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
* IReactionProcess type = new RadicalSiteRrGammaReaction();
* 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 2006-10-20
* @cdk.module reaction
* @cdk.githash
* @cdk.set reaction-types
*
* @see RadicalSiteRearrangementMechanism
**/
@TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteRrGammaReactionTest")
public class RadicalSiteRrGammaReaction extends ReactionEngine implements IReactionProcess{
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(RadicalSiteRrGammaReaction.class);
/**
* Constructor of the RadicalSiteRrGammaReaction object
*
*/
public RadicalSiteRrGammaReaction(){
}
/**
* Gets the specification attribute of the RadicalSiteRrGammaReaction object
*
*@return The specification value
*/
@TestMethod("testGetSpecification")
public ReactionSpecification getSpecification() {
return new ReactionSpecification(
"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#RadicalSiteRrGamma",
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: RadicalSiteRrGammaReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("RadicalSiteRrGammaReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("RadicalSiteRrGammaReaction don't expects agents");
}
IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
IMolecule reactant = reactants.getMolecule(0);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactant);
CDKHueckelAromaticityDetector.detectAromaticity(reactant);
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.findAllRings((Molecule) reactant);
for (int ir = 0; ir < ringSet.getAtomContainerCount(); ir++) {
Ring ring = (Ring)ringSet.getAtomContainer(ir);
for (int jr = 0; jr < ring.getAtomCount(); jr++) {
IAtom aring = ring.getAtom(jr);
aring.setFlag(CDKConstants.ISINRING, true);
}
}
/* 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);
HOSECodeGenerator hcg = new HOSECodeGenerator();
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& reactant.getConnectedSingleElectronsCount(atomi) == 1) {
hcg.getSpheres((Molecule) reactant, atomi, 4, true);
List<IAtom> atom1s = hcg.getNodesInSphere(4);
hcg.getSpheres((Molecule) reactant, atomi, 5, true);
Iterator<IAtom> atomls = hcg.getNodesInSphere(5).iterator();
while(atomls.hasNext()){
IAtom atoml = atomls.next();
if(atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER) && !atoml.getFlag(CDKConstants.ISINRING) &&
(atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0 && !atoml.equals("H") &&
reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE){
Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
while(atomRs.hasNext()){
IAtom atomR = atomRs.next();
if(atom1s.contains(atomR))
continue;
if(reactant.getBond(atomR, atoml).getFlag(CDKConstants.REACTIVE_CENTER) &&
atomR.getFlag(CDKConstants.REACTIVE_CENTER) &&
(atomR.getFormalCharge() == CDKConstants.UNSET ? 0 : atomR.getFormalCharge()) == 0){
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
atomList.add(atomR);
atomList.add(atomi);
atomList.add(atoml);
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(reactant.getBond(atomR, atoml));
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*]-(C)_2-C3[R]
* <pre>
* C: Atom with single electron
* C5: Atom with the R to move
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
HOSECodeGenerator hcg = new HOSECodeGenerator();
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
if(reactant.getConnectedSingleElectronsCount(atomi) == 1) {
hcg.getSpheres((Molecule) reactant, atomi, 4, true);
List<IAtom> atom1s = hcg.getNodesInSphere(4);
hcg.getSpheres((Molecule) reactant, atomi, 5, true);
Iterator<IAtom> atomls = hcg.getNodesInSphere(5).iterator();
while(atomls.hasNext()){
IAtom atoml = atomls.next();
if(atoml != null && !atoml.getFlag(CDKConstants.ISINRING) &&
(atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0 && !atoml.equals("H") &&
reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE){
Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
while(atomRs.hasNext()){
IAtom atomR = atomRs.next();
if(atom1s.contains(atomR))
continue;
if((atomR.getFormalCharge() == CDKConstants.UNSET ? 0 : atomR.getFormalCharge()) == 0){
atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
atoml.setFlag(CDKConstants.REACTIVE_CENTER,true);
atomR.setFlag(CDKConstants.REACTIVE_CENTER,true);
reactant.getBond(atomR, atoml).setFlag(CDKConstants.REACTIVE_CENTER,true);
}
}
}
}
}
}
}
}