reaction.java

化学图形处理软件

/* $Revision: 7636 $ $Author: egonw $ $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 *
 * Copyright (C) 2003-2007  Egon Willighagen <[e-mail]>
 * 
 * Contact: [e-mail]
 * 
 * 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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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;

import java.io.Serializable;
import java.util.Hashtable;

import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IReaction;

/**
 * Represents the idea of a chemical reaction. The reaction consists of 
 * a set of reactants and a set of products.
 *
 * <p>The class mostly represents abstract reactions, such as 2D diagrams,
 * and is not intended to represent reaction trajectories. Such can better
 * be represented with a ChemSequence.
 *
 * @cdk.module data
 *
 * @author      Egon Willighagen <[e-mail]>
 * @cdk.created 2003-02-13
 * @cdk.keyword reaction
 */
public class Reaction extends ChemObject implements Serializable, IReaction, Cloneable {

    /**
     * Determines if a de-serialized object is compatible with this class.
     *
     * This value must only be changed if and only if the new version
     * of this class is imcompatible with the old version. See Sun docs
     * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
     * /serialization/spec/version.doc.html>details</a>.
	 */
	private static final long serialVersionUID = -554752558363533678L;

	protected int growArraySize = 3;

    protected org.openscience.cdk.interfaces.IMoleculeSet reactants;
    protected org.openscience.cdk.interfaces.IMoleculeSet products;
    /** These are the used solvent, catalysist etc that normally appear above
        the reaction arrow */
    protected org.openscience.cdk.interfaces.IMoleculeSet agents;
    
    protected org.openscience.cdk.interfaces.IMapping[] map;
    protected int mappingCount;
    
    private int reactionDirection;
    
    /**
     * Constructs an empty, forward reaction.
     */
    public Reaction() {
        this.reactants = new MoleculeSet();
        this.products = new MoleculeSet();
        this.agents = new MoleculeSet();
        this.map = new Mapping[growArraySize];
        mappingCount = 0;
        reactionDirection = FORWARD;
    }
    
    /**
     * Returns the number of reactants in this reaction.
     *
     * @return The number of reactants in this reaction
     */
    public int getReactantCount() {
        return reactants.getAtomContainerCount();
    }
    
    /**
     * Returns the number of products in this reaction.
     *
     * @return The number of products in this reaction
     */
    public int getProductCount() {
        return products.getAtomContainerCount();
    }

    /**
     * Returns a MoleculeSet containing the reactants in this reaction.
     *
     * @return A MoleculeSet containing the reactants in this reaction
     * @see    #setReactants
     */
    public org.openscience.cdk.interfaces.IMoleculeSet getReactants() {
        return (MoleculeSet)reactants;
    }

    /**
     * Assigns a MoleculeSet to the reactants in this reaction.
     *
     * @param setOfMolecules The new set of reactants
     * @see   #getReactants
     */
    public void setReactants(org.openscience.cdk.interfaces.IMoleculeSet setOfMolecules) {
        reactants = setOfMolecules;
	notifyChanged();
    }
	
    /**
     * Returns a MoleculeSet containing the products of this reaction.
     *
     * @return A MoleculeSet containing the products in this reaction
     * @see    #setProducts
     */
    public org.openscience.cdk.interfaces.IMoleculeSet getProducts() {
        return (MoleculeSet)products;
    }
    
	/**
     * Assigns a MoleculeSet to the products of this reaction.
     *
     * @param setOfMolecules The new set of products
     * @see   #getProducts
     */
    public void setProducts(org.openscience.cdk.interfaces.IMoleculeSet setOfMolecules) {
        products = setOfMolecules;
	notifyChanged();
    }
	
    /**
     * Returns a MoleculeSet containing the agents in this reaction.
     *
     * @return A MoleculeSet containing the agents in this reaction
     * @see    #addAgent
     */
    public org.openscience.cdk.interfaces.IMoleculeSet getAgents() {
        return (MoleculeSet)agents;
    }
    
    /**
     * Returns the mappings between the reactant and the product side.
     *
     * @return An Iterator to the Mappings.
     * @see    #addMapping
     */
    public java.util.Iterator mappings() {
        Mapping[] returnMappings = new Mapping[mappingCount];
        System.arraycopy(this.map, 0, returnMappings, 0, returnMappings.length);
        return new MappingIterator();
    }
    
    /**
     * The inner Mapping Iterator class.
     *
     */
    private class MappingIterator implements java.util.Iterator {

        private int pointer = 0;
    	
        public boolean hasNext() {
            if (pointer < mappingCount) return true;
	    return false;
        }

        public Object next() {
            return map[pointer++];
        }

        public void remove() {
            removeMapping(--pointer);
        }
    	
    }
    
    /**
     * Adds a reactant to this reaction.
     *
     * @param reactant   Molecule added as reactant to this reaction
     * @see   #getReactants
     */
    public void addReactant(org.openscience.cdk.interfaces.IMolecule reactant) {
        addReactant(reactant, 1.0);
	/* notifyChanged() is called by 
	   addReactant(Molecule reactant, double coefficient) */
    }
    
    /**
     * Adds an agent to this reaction.
     *
     * @param agent   Molecule added as agent to this reaction
     * @see   #getAgents
     */
    public void addAgent(org.openscience.cdk.interfaces.IMolecule agent) {
        agents.addAtomContainer(agent);
	notifyChanged();
    }

    /**
     * Adds a reactant to this reaction with a stoichiometry coefficient.
     *
     * @param reactant    Molecule added as reactant to this reaction
     * @param coefficient Stoichiometry coefficient for this molecule
     * @see   #getReactants
     */
    public void addReactant(org.openscience.cdk.interfaces.IMolecule reactant, double coefficient) {
        reactants.addAtomContainer(reactant, coefficient);
	notifyChanged();
    }
    
    /**
     * Adds a product to this reaction.
     *
     * @param product    Molecule added as product to this reaction
     * @see   #getProducts
     */
    public void addProduct(org.openscience.cdk.interfaces.IMolecule product) {
        this.addProduct(product, 1.0);
	/* notifyChanged() is called by 
	addProduct(Molecule product, double coefficient)*/
    }