SharingChargeSBReaction.java

/*
 *  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  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.HeterolyticCleavageMechanism;
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 => A| + [B+]. Due to 
 * deficiency of charge of the atom A, the double bond is displaced to atom A.</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 HeterolyticCleavageMechanism class</p>
 * 
 * <pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new SharingChargeSBReaction();
 *  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 HeterolyticCleavageMechanism
 **/
@TestClass(value="org.openscience.cdk.reaction.type.SharingChargeSBReactionTest")
public class SharingChargeSBReaction extends ReactionEngine implements IReactionProcess{
	private static ILoggingTool logger =
	    LoggingToolFactory.createLoggingTool(SharingChargeSBReaction.class);

	/**
	 * Constructor of the SharingChargeSBReaction object.
	 *
	 */
	public SharingChargeSBReaction(){
	}
	/**
	 *  Gets the specification attribute of the SharingChargeSBReaction object
	 *
	 *@return    The specification value
	 */
    @TestMethod("testGetSpecification")
	public ReactionSpecification getSpecification() {
		return new ReactionSpecification(
				"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#SharingChargeSB",
				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: SharingChargeSBReaction");
		
		if (reactants.getMoleculeCount() != 1) {
			throw new CDKException("SharingChargeSBReaction only expects one reactant");
		}
		if (agents != null) {
			throw new CDKException("SharingChargeSBReaction 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 ){

				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() == 0)
							if(reactant.getConnectedSingleElectronsCount(atomj) == 0){
								
								ArrayList<IAtom> atomList = new ArrayList<IAtom>();
			                	atomList.add(atomj);
			                	atomList.add(atomi);
			                	ArrayList<IBond> bondList = new ArrayList<IBond>();
			                	bondList.add(bondi);

								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. 
	 * <pre>
	 * A: Atom with positive charge
	 * -: single bond
	 * B: 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 ){

				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() == 0)
							if(reactant.getConnectedSingleElectronsCount(atomj) == 0){
								atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
								bondi.setFlag(CDKConstants.REACTIVE_CENTER,true);
								atomj.setFlag(CDKConstants.REACTIVE_CENTER,true);
						}
					}
				}
			}
		}
	}
}