/* $Revision$ $Author$ $Date$
*
* 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")
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")
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 */
for(IAtom atom:molecule.atoms()){
IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
if(bond2.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;
}
}