RemovingSEofBMechanism.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.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.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;

/**
 * This mechanism extracts a single electron from a bonding orbital which located in
 * an bond. It could have single, double as triple order. It returns the 
 * reaction mechanism which has been cloned the IMolecule with a decrease 
 * of the order of the bond and a ISingleElectron more.
 * 
 * @author         miguelrojasch
 * @cdk.created    2008-02-10
 * @cdk.module     reaction
 *
 */
@TestClass(value="org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanismTest")
public class RemovingSEofBMechanism 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 atoms.
     *                    The first atom receives the charge and the second the single electron
     * @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")
	public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
		CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(moleculeSet.getBuilder(), CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS);
		if (moleculeSet.getMoleculeCount() != 1) {
			throw new CDKException("RemovingSEofBMechanism only expects one IMolecule");
		}
		if (atomList.size() != 2) {
			throw new CDKException("RemovingSEofBMechanism expects two atoms in the ArrayList");
		}
		if (bondList.size() != 1) {
			throw new CDKException("RemovingSEofBMechanism only expects 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);
		IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
		IAtom atom2 = atomList.get(1);
		IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
		IBond bond1 = bondList.get(0);
		int posBond1 = molecule.getBondNumber(bond1);
		
		if(bond1.getOrder() == IBond.Order.SINGLE)
			reactantCloned.removeBond(reactantCloned.getBond(posBond1));    
        else
        	BondManipulator.decreaseBondOrder(reactantCloned.getBond(posBond1));
		
		int charge = atom1C.getFormalCharge();
		atom1C.setFormalCharge(charge+1);
		reactantCloned.addSingleElectron(new SingleElectron(atom2C));

		// check if resulting atom type is reasonable
		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;
		
		IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
		reaction.addReactant(molecule);
		
		/* mapping */
		for(IAtom atom:molecule.atoms()){
			IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
			reaction.addMapping(mapping);
	    }
		if(bond1.getOrder() != IBond.Order.SINGLE) {
        	reaction.addProduct(reactantCloned);
        }else{
	        IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
			for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){
				reaction.addProduct(moleculeSetP.getMolecule(z));
			}
        }
        
		return reaction;
	}

}