/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2008 Miguel Rojas <miguelrojasch@users.sf.net>
*
* 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.type;
import java.util.ArrayList;
import java.util.Iterator;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionEngine;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.reaction.mechanism.AdductionLPMechanism;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* <p>IReactionProcess which produces an adduction of the Sodium.
* As most commonly encountered, this reaction results in the formal migration
* of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond</p>
*
* <pre>[X-] + [Na+] => X -Na</pre>
* <pre>|X + [Na+] => [X+]-Na</pre>
*
* <p>Below you have an example how to initiate the mechanism.</p>
* <p>It is processed by the AdductionLPMechanism class</p>
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
* IReactionProcess type = new AdductionSodiumLPReaction();
* Object[] params = {Boolean.FALSE};
type.setParameters(params);
* IReactionSet setOfReactions = type.initiate(setOfReactants, null);
* </pre>
*
* <p>We have the possibility to localize the reactive center. Good method if you
* want to specify the reaction in a fixed point.</p>
* <pre>atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);</pre>
* <p>Moreover you must put the parameter Boolean.TRUE</p>
* <p>If the reactive center is not specified then the reaction process will
* try to find automatically the possible reaction centers.</p>
*
*
* @author Miguel Rojas
*
* @cdk.created 2008-02-11
* @cdk.module reaction
* @cdk.set reaction-types
*
* @see AdductionLPMechanism
**/
@TestClass(value="org.openscience.cdk.reaction.type.AdductionSodiumLPReactionTest")
public class AdductionSodiumLPReaction extends ReactionEngine implements IReactionProcess{
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(AdductionSodiumLPReaction.class);
/**
* Constructor of the AdductionSodiumLPReaction object.
*
*/
public AdductionSodiumLPReaction(){
}
/**
* Gets the specification attribute of the AdductionSodiumLPReaction object.
*
*@return The specification value
*/
@TestMethod("testGetSpecification")
public ReactionSpecification getSpecification() {
return new ReactionSpecification(
"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#AdductionSodiumLP",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Initiate process.
* It is needed to call the addExplicitHydrogensToSatisfyValency
* from the class tools.HydrogenAdder.
*
*@param reactants reactants of the reaction
*@param agents agents of the reaction (Must be in this case null)
*
*@exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
logger.debug("initiate reaction: AdductionSodiumLPReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("AdductionSodiumLPReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("AdductionSodiumLPReaction don't expects agents");
}
IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
IMolecule reactant = reactants.getMolecule(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if( ipr != null && !ipr.isSetParameter())
setActiveCenters(reactant);
if(AtomContainerManipulator.getTotalCharge(reactant) > 0)
return setOfReactions;
Iterator<IAtom> atoms = reactant.atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next(); // Atom pos 1
if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atomi.getFormalCharge() == CDKConstants.UNSET ? 0 : atomi.getFormalCharge()) <= 0
&& reactant.getConnectedLonePairsCount(atomi) > 0 && reactant.getConnectedSingleElectronsCount(atomi) == 0){
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
atomList.add(atomi);
IAtom atomH = reactant.getBuilder().newAtom("Na");
atomH.setFormalCharge(1);
atomList.add(atomH);
IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
moleculeSet.addMolecule(reactant);
IMolecule adduct = reactant.getBuilder().newMolecule();
adduct.addAtom(atomH);
moleculeSet.addMolecule(adduct);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, null);
if(reaction == null)
continue;
else
setOfReactions.addReaction(reaction);
}
}
return setOfReactions;
}
/**
* set the active center for this molecule.
* The active center will be those which correspond with X=Y-Z-Na.
* <pre>
* [X-]
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
if(AtomContainerManipulator.getTotalCharge(reactant) > 0)
return;
Iterator<IAtom> atoms = reactant.atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next(); // Atom pos 1
if((atomi.getFormalCharge() == CDKConstants.UNSET ? 0 : atomi.getFormalCharge()) <= 0
&& reactant.getConnectedLonePairsCount(atomi) > 0
&& reactant.getConnectedSingleElectronsCount(atomi) == 0){
atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
}
}
}
}