AtomContainerBondPermutor.java

/*
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 *  Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 *
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package org.openscience.cdk.graph;

import java.util.Iterator;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;


/**
 * This class allows to iterate trough the set of all possible
 * permutations of the bond order in a given atom container. 
 * It allows to check for a dependency of algorithm results 
 * on the bond order.
 *
 * <p>The permutation code here is based on a pseudo code example 
 * on a tutorial site created and maintained by Phillip P. Fuchs:
 * <a href="http://www.geocities.com/permute_it/pseudo2.html">http://www.geocities.com/permute_it/pseudo2.html</a>.
 * 
 *@author         steinbeck
 * @cdk.githash
 *@cdk.created    2005-05-04
 *@cdk.keyword    permutation
 */
public class AtomContainerBondPermutor extends AtomContainerPermutor
{

    public AtomContainerBondPermutor(IAtomContainer ac)
    {
        setAtomContainer(ac);
        N = atomContainer.getBondCount();
        initBookkeeping();
        initObjectArray();
    }

    public void initObjectArray() {
        Iterator bonds = atomContainer.bonds().iterator();
        objects = new Object[atomContainer.getBondCount()];
        int i = 0;
        while (bonds.hasNext()) {
            objects[i] = bonds.next();
            i++;
        }
    }

    IAtomContainer makeResult()
    {
        IBond[] bonds = new IBond[objects.length];
        for (int f = 0; f < objects.length; f++)
        {
            bonds[f] = ((IBond)objects[f]);
        }
        IAtomContainer ac = atomContainer.getBuilder().newAtomContainer(atomContainer);
        ac.setBonds(bonds);
        IAtomContainer clone = null;
        try {
            clone = (IAtomContainer)ac.clone();
        } catch (CloneNotSupportedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return clone;
    }

}