/* $Revision$ $Author$ $Date$
*
* 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.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.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.reaction.IReactionMechanism;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This mechanism extracts a single electron from a non-bonding orbital which located in
* a ILonePair container. It returns the reaction mechanism which has been cloned the
* IMolecule with an ILonPair electron less and an ISingleElectron more.
*
* @author miguelrojasch
* @cdk.created 2008-02-10
* @cdk.module reaction
*
*/
@TestClass(value="org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanismTest")
public class RemovingSEofNBMechanism 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 one atom
* @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());
if (moleculeSet.getMoleculeCount() != 1) {
throw new CDKException("RemovingSEofNBMechanism only expects one IMolecule");
}
if (atomList.size() != 1) {
throw new CDKException("RemovingSEofNBMechanism only expects one atom in the ArrayList");
}
if (bondList != null) {
throw new CDKException("RemovingSEofNBMechanism don't expect any 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);
}
// remove one lone pair electron and substitute with one single electron and charge 1.
int posAtom = molecule.getAtomNumber(atomList.get(0));
List<ILonePair> lps = reactantCloned.getConnectedLonePairsList(reactantCloned.getAtom(posAtom));
reactantCloned.removeLonePair(lps.get(lps.size() - 1));
reactantCloned.addSingleElectron(new SingleElectron(reactantCloned.getAtom(posAtom)));
int charge = reactantCloned.getAtom(posAtom).getFormalCharge();
reactantCloned.getAtom(posAtom).setFormalCharge(charge+1);
// check if resulting atom type is reasonable
reactantCloned.getAtom(posAtom).setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, reactantCloned.getAtom(posAtom));
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);
}
reaction.addProduct(reactantCloned);
return reaction;
}
}