/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.IBond;
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.HeterolyticCleavageMechanism;
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;
/**
* <p>IReactionProcess which a bond is broken displacing the electron to one of the
* atoms. The mechanism will produce one atom with excess of charge and the other one deficiency.
* Depending of the bond order, the bond will be removed or simply the order decreased.
* As there are two directions for displacing a bond in a polar manner,
* each case is investigated twice:</p>
*
* <pre>A-B => [A+] + |[B-]</pre>
* <pre>A-B => |[A-] + [B+]</pre>
*
* <p>It will not be created structures no possible, e.g; C=O => [C-][O+].</p>
* <p>Below you have an example how to initiate the mechanism.</p>
* <p>It is processed by the HeterolyticCleavageMechanism class</p>
* <pre>
* IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
* setOfReactants.addMolecule(new Molecule());
* IReactionProcess type = new HeterolyticCleavageSBReaction();
* 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 2006-06-09
* @cdk.module reaction
* @cdk.githash
* @cdk.set reaction-types
*
* @see HeterolyticCleavageMechanism
**/
@TestClass(value="org.openscience.cdk.reaction.type.HeterolyticCleavageSBReactionTest")
public class HeterolyticCleavageSBReaction extends ReactionEngine implements IReactionProcess{
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(HeterolyticCleavageSBReaction.class);
/**
* Constructor of the HeterolyticCleavageSBReaction object.
*
*/
public HeterolyticCleavageSBReaction(){
}
/**
* Gets the specification attribute of the HeterolyticCleavageSBReaction object.
*
*@return The specification value
*/
@TestMethod("testGetSpecification")
public ReactionSpecification getSpecification() {
return new ReactionSpecification(
"http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#HeterolyticCleavageSB",
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: HeterolyticCleavageSBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavageSBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavageSBReaction 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);
Iterator<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if(bondi.getFlag(CDKConstants.REACTIVE_CENTER) && bondi.getOrder() == IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0 && reactant.getConnectedSingleElectronsCount(atom2) == 0){
/**/
for (int j = 0; j < 2; j++){
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0){
atomList.add(atom1);
atomList.add(atom2);
}else{
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
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 A-B. If
* the bond is simple, it will be broken forming two fragments
* <pre>
* A: Atom
* #/=/-: bond
* B: Atom
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
Iterator<IBond> bonds = reactant.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = bonds.next();
IAtom atom1 = bond.getAtom(0);
IAtom atom2 = bond.getAtom(1);
if( bond.getOrder() == IBond.Order.SINGLE
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0 && reactant.getConnectedSingleElectronsCount(atom2) == 0){
atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
}
}
}
}