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AtomContainerAtomPermutor.java
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AtomContainerAtomPermutor.java
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/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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
* 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.graph;
import java.util.Iterator;
import org.openscience.cdk.Atom;
import org.openscience.cdk.interfaces.IAtom;
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
*/
public class AtomContainerAtomPermutor extends AtomContainerPermutor
{
public AtomContainerAtomPermutor(IAtomContainer ac)
{
setAtomContainer(ac);
N = atomContainer.getAtomCount();
initBookkeeping();
initObjectArray();
}
public void initObjectArray()
{
Iterator<IAtom> atoms = atomContainer.atoms().iterator();
objects = new Object[atomContainer.getAtomCount()];
int count = -1;
while (atoms.hasNext())
{
objects[++count] = atoms.next();
}
}
IAtomContainer 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);
ac.setAtoms(atoms);
IAtomContainer clone = null;
try {
clone = (IAtomContainer)ac.clone();
} catch (CloneNotSupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return clone;
}
}