/* 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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
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;

import java.util.ArrayList;
import java.util.Iterator;

/**
 * <p>IReactionProcess which produces a protonation.
 * 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-] + [H+] =&gt; X -H</pre>
 * <pre>|X + [H+]   =&gt; [X+]-H</pre>
 *
 * <p>Below you have an example how to initiate the mechanism.</p>
 * <p>It is processed by the AdductionLPMechanism class</p>
 * <pre>
 *  IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet();
 *  setOfReactants.addAtomContainer(new AtomContainer());
 *  IReactionProcess type = new AdductionProtonLPReaction();
 *  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.githash
 *
 * @see AdductionLPMechanism
 **/
public class AdductionProtonLPReaction extends ReactionEngine implements IReactionProcess {

    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(AdductionProtonLPReaction.class);

    /**
     * Constructor of the AdductionProtonLPReaction object.
     *
     */
    public AdductionProtonLPReaction() {}

    /**
     *  Gets the specification attribute of the AdductionProtonLPReaction object.
     *
     *@return    The specification value
     */
    @Override
    public ReactionSpecification getSpecification() {
        return new ReactionSpecification(
                "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#AdductionProtonLP", this
                        .getClass().getName(), "$Id$", "The Chemistry Development Kit");
    }

    /**
     *  Initiate process.
     *  It is needed to call the addExplicitHydrogensToSatisfyValency
     *  from the class tools.HydrogenAdder.
     *
     *
     *@exception  CDKException  Description of the Exception

     * @param  reactants         reactants of the reaction
    * @param  agents            agents of the reaction (Must be in this case null)
     */
    @Override
    public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException {

        logger.debug("initiate reaction: AdductionProtonLPReaction");

        if (reactants.getAtomContainerCount() != 1) {
            throw new CDKException("AdductionProtonLPReaction only expects one reactant");
        }
        if (agents != null) {
            throw new CDKException("AdductionProtonLPReaction don't expects agents");
        }

        IReactionSet setOfReactions = reactants.getBuilder().newInstance(IReactionSet.class);
        IAtomContainer reactant = reactants.getAtomContainer(0);

        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().newInstance(IAtom.class, "H");
                atomH.setFormalCharge(1);
                atomList.add(atomH);

                IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class);
                moleculeSet.addAtomContainer(reactant);
                IAtomContainer adduct = reactant.getBuilder().newInstance(IAtomContainer.class);
                adduct.addAtom(atomH);
                moleculeSet.addAtomContainer(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-H.
     * <pre>
     * [X-]
     *  </pre>
     *
     * @param reactant The molecule to set the activity
     * @throws CDKException
     */
    private void setActiveCenters(IAtomContainer 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);

            }
        }
    }
}
