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RearrangementChargeMechanism.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 2008  Miguel Rojas <miguelrojasch@yahoo.es>
 * 
 * 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.mechanism;

import java.util.ArrayList;
import java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.LonePair;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.BondManipulator;

/**
 * <p>This mechanism displaces the charge(radical, charge + or charge -) because of
 * a double bond which is associated. 
 * It returns the reaction mechanism which has been cloned the IMolecule.</p>
 * <p>This reaction could be represented as [A*]-Y=Z => A=Z-[Y*]</p>
 * 
 * @author         miguelrojasch
 * @cdk.created    2008-02-10
 * @cdk.module     reaction
 *
 */
@TestClass(value="org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanismTest")
00060 public class RearrangementChargeMechanism implements IReactionMechanism{

      /** 
     * Initiates the process for the given mechanism. The atoms to apply are mapped between
     * reactants and products. 
     *
     * @param moleculeSet The IMolecule to apply the mechanism
     * @param atomList    The list of atoms taking part in the mechanism. Only allowed two three.
     *                    The first atom is the atom which must contain the charge to be moved, the second 
     *                    is the atom which is in the middle and the third is the atom which acquires the new charge
     * @param bondList    The list of bonds taking part in the mechanism. Only allowed two bond.
     *                                The first bond is the bond to increase the order and the second is the bond
     *                              to decrease the order
     *                                It is the bond which is moved
     * @return            The Reaction mechanism
     * 
       */
    @TestMethod(value="testInitiate_IMoleculeSet_ArrayList_ArrayList")
00078       public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
            CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(moleculeSet.getBuilder());
            if (moleculeSet.getMoleculeCount() != 1) {
                  throw new CDKException("RearrangementChargeMechanism only expects one IMolecule");
            }
            if (atomList.size() != 3) {
                  throw new CDKException("RearrangementChargeMechanism expects three atoms in the ArrayList");
            }
            if (bondList.size() != 2) {
                  throw new CDKException("RearrangementChargeMechanism only expect one bond in the ArrayList");
            }
            IMolecule molecule = moleculeSet.getMolecule(0);
            IMolecule reactantCloned;
            try {
                  reactantCloned = (IMolecule) molecule.clone();
            } catch (CloneNotSupportedException e) {
                  throw new CDKException("Could not clone IMolecule!", e);
            }
            IAtom atom1 = atomList.get(0);// Atom with the charge
            IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
            IAtom atom2 = atomList.get(1);// Atom not participating
            IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
            IAtom atom3 = atomList.get(2);// Atom which acquires the charge
            IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
            IBond bond1 = bondList.get(0);// Bond with single bond
            int posBond1 = molecule.getBondNumber(bond1);
            IBond bond2 = bondList.get(1);// Bond with double bond
            int posBond2 = molecule.getBondNumber(bond2);
            
      BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
      if(bond2.getOrder() == IBond.Order.SINGLE)
                  reactantCloned.removeBond(reactantCloned.getBond(posBond2));    
            else
            BondManipulator.decreaseBondOrder(reactantCloned.getBond(posBond2));
            
      //Depending of the charge moving (radical, + or -) there is a different situation
      if(reactantCloned.getConnectedSingleElectronsCount(atom1C) > 0){
            List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
            reactantCloned.removeSingleElectron(selectron.get(selectron.size() -1));            
            
            reactantCloned.addSingleElectron(new SingleElectron(atom3C));
            
      }else if(atom1C.getFormalCharge() > 0){
            int charge = atom1C.getFormalCharge();
            atom1C.setFormalCharge(charge-1);
            
            charge = atom3C.getFormalCharge();
            atom3C.setFormalCharge(charge+1);
      
      }else if(atom1C.getFormalCharge() < 1){
            int charge = atom1C.getFormalCharge();
            atom1C.setFormalCharge(charge+1);
            List<ILonePair> ln = reactantCloned.getConnectedLonePairsList(atom1C);
            reactantCloned.removeLonePair(ln.get(ln.size() -1));  
            atom1C.setFlag(CDKConstants.ISAROMATIC,false);  
            
            charge = atom3C.getFormalCharge();
            atom3C.setFormalCharge(charge-1);
            reactantCloned.addLonePair(new LonePair(atom3C));
            atom3C.setFlag(CDKConstants.ISAROMATIC,false);
      }else
            return null;
      
      atom1C.setHybridization(null);
            atom3C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
            
            IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
            if (type == null) return null;

            type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
            if (type == null) return null;
            
            IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
            reaction.addReactant(molecule);
            
            /* mapping */
            IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom1, atom1C);
        reaction.addMapping(mapping);
        mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom2, atom2C);
        reaction.addMapping(mapping);
        mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom3, atom3C);
        reaction.addMapping(mapping);
        mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1));
      reaction.addMapping(mapping);
      if(bond2.getOrder() != IBond.Order.SINGLE) {
            mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond2, reactantCloned.getBond(posBond2));
            reaction.addMapping(mapping);
            reaction.addProduct(reactantCloned);
        } else{
              IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
                  for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){
                        reaction.addProduct(moleculeSetP.getMolecule(z));
                  }
        }
      
            return reaction;
      }

}

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