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

import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.interfaces.IAtomContainer;

 * This class allows to iterate trough the set of all possible
 * permutations of the atom order in a given atom container. 
 * It allows to check for a dependency of algorithm results 
 * on the atom 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
00051 public class AtomContainerAtomPermutor extends AtomContainerPermutor
      public AtomContainerAtomPermutor(AtomContainer ac)
            N = atomContainer.getAtomCount();
      public void initObjectArray()
            java.util.Iterator atoms = atomContainer.atoms().iterator();
            objects = new Object[atomContainer.getAtomCount()];
            int count = -1;
            while (atoms.hasNext())
                  objects[++count] = atoms.next();    
      AtomContainer makeResult()
            Atom[] atoms = new Atom[objects.length];
            for (int f = 0; f < objects.length; f++)
                  atoms[f] = ((Atom)objects[f]);      
            IAtomContainer ac = atomContainer.getBuilder().newAtomContainer(atomContainer);
            AtomContainer clone = null;
            try {
                  clone = (AtomContainer)ac.clone();
            } catch (CloneNotSupportedException e) {
                  // TODO Auto-generated catch block
            return clone;

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