Logo Search packages:      
Sourcecode: cdk version File versions  Download package

AdductionPBMechanism.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 org.openscience.cdk.DefaultChemObjectBuilder;
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.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
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.reaction.IReactionMechanism;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.BondManipulator;

/**
 * <p>This mechanism adduct together two fragments due to a double bond. 
 * The second fragment will be deficient in charge.
 * It returns the reaction mechanism which has been cloned the IMolecule.</p>
 * <p>This reaction could be represented as A=B + [C+] => [A+]-B-C</p>
 * 
 * 
 * @author         miguelrojasch
 * @cdk.created    2008-02-10
 * @cdk.module     reaction
 *
 */
@TestClass(value="org.openscience.cdk.reaction.mechanism.AdductionPBMechanismTest")
00055 public class AdductionPBMechanism implements IReactionMechanism{

      /** 
     * Initiates the process for the given mechanism. The atoms and bonds 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 three atoms
     * @param bondList    The list of bonds taking part in the mechanism. Only allowed one bond
     * 
     * @return            The Reaction mechanism
     * 
       */
    @TestMethod(value="testInitiate_IMoleculeSet_ArrayList_ArrayList")
00069       public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
            CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(moleculeSet.getBuilder());
            if (moleculeSet.getMoleculeCount() != 2) {
                  throw new CDKException("AdductionPBMechanism expects two IMolecule's");
            }
            if (atomList.size() != 3) {
                  throw new CDKException("AdductionPBMechanism expects two atoms in the ArrayList");
            }
            if (bondList.size() != 1) {
                  throw new CDKException("AdductionPBMechanism don't expect bonds in the ArrayList");
            }
            IMolecule molecule = moleculeSet.getMolecule(0);
            IMolecule reactantCloned;
            try {
                  reactantCloned = (IMolecule) moleculeSet.getMolecule(0).clone();
                  reactantCloned.add((IAtomContainer) moleculeSet.getMolecule(1).clone());
            } catch (CloneNotSupportedException e) {
                  throw new CDKException("Could not clone IMolecule!", e);
            }
            IAtom atom1 = atomList.get(0);// Atom 1: to be deficient in charge 
            IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
            IAtom atom2 = atomList.get(1);// Atom 2: receive the adduct
            IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
            IAtom atom3 = atomList.get(2);// Atom 2: deficient in charge
            IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3)+moleculeSet.getMolecule(0).getAtomCount()+1);
            IBond bond1 = bondList.get(0);
            int posBond1 = moleculeSet.getMolecule(0).getBondNumber(bond1);
            
      BondManipulator.decreaseBondOrder(reactantCloned.getBond(posBond1));
      IBond newBond = molecule.getBuilder().newBond(atom2C, atom3C, IBond.Order.SINGLE);
      reactantCloned.addBond(newBond);
      
      int charge = atom1C.getFormalCharge();
      atom1C.setFormalCharge(charge+1);
      atom1C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
            IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
            if (type == null) return null;

            atom2C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
            type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
            if (type == null) return null;
            
            charge = atom3C.getFormalCharge();
      atom3C.setFormalCharge(charge-1);
      atom3C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
            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(bond1, reactantCloned.getBond(posBond1));
        reaction.addMapping(mapping);
        
      reaction.addProduct(reactantCloned);
      
            return reaction;
      }

}

Generated by  Doxygen 1.6.0   Back to index