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Re-write of the atom container permutation classes. An extra class 'P…
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…ermutor' is now the base class for permutations, and contains some more functionality than before.

Signed-off-by: maclean <gilleain.torrance@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@gilleain @egonw
gilleain authored and egonw committed Sep 18, 2011
1 parent 04adfca commit acd8e9b
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Showing 4 changed files with 204 additions and 242 deletions.
109 changes: 47 additions & 62 deletions src/main/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
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@@ -1,10 +1,4 @@
/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
/* Copyright (C) 2009 Gilleain Torrance <gilleain.torrance@gmail.com>
*
* Contact: cdk-devel@lists.sourceforge.net
*
Expand All @@ -29,67 +23,58 @@
*/
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>.
* An atom container atom permutor that uses ranking and unranking to calculate
* the next permutation in the series.</p>
*
* <p>Typical use:<pre>
* AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(container);
* while (permutor.hasNext()) {
* IAtomContainer permutedContainer = permutor.next();
* ...
* }</pre>
*
*@author steinbeck
* @cdk.githash
*@cdk.created 2005-05-04
*@cdk.keyword permutation
* @author maclean
* @cdk.created 2009-09-09
* @cdk.keyword permutation
* @cdk.module standard
*/
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().newInstance(IAtomContainer.class,atomContainer);
ac.setAtoms(atoms);
IAtomContainer clone = null;
try {
clone = (IAtomContainer)ac.clone();
} catch (CloneNotSupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return clone;
}

public class AtomContainerAtomPermutor extends AtomContainerPermutor {

/**
* A permutor wraps the original atom container, and produces cloned
* (and permuted!) copies on demand.
*
* @param atomContainer
*/
public AtomContainerAtomPermutor(IAtomContainer atomContainer) {
super(atomContainer.getAtomCount(), atomContainer);
}

/**
* Generate the atom container with this permutation of the atoms.
*
* @param permutation the permutation to use
* @return the
*/
public IAtomContainer containerFromPermutation(int[] permutation) {
try {
IAtomContainer permutedContainer =
(IAtomContainer) atomContainer.clone();
IAtom[] atoms = new IAtom[atomContainer.getAtomCount()];
for (int i = 0; i < atomContainer.getAtomCount(); i++) {
atoms[permutation[i]] = permutedContainer.getAtom(i);
}
permutedContainer.setAtoms(atoms);
return permutedContainer;
} catch (CloneNotSupportedException c) {
return null;
}
}

}

128 changes: 57 additions & 71 deletions src/main/org/openscience/cdk/graph/AtomContainerBondPermutor.java
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@@ -1,93 +1,79 @@
/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
/* Copyright (C) 2009 Gilleain Torrance <gilleain.torrance@gmail.com>
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
* Contact: cdk-devel@lists.sourceforge.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.
* 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 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.
* 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.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>.
* This class allows the user to iterate through the set of all possible
* permutations of the bond order in a given atom container. This provides a
* means to check the dependency of an algorithm's results on the bond order of
* the input atom container.
*
* <p>Typical use:<pre>
* AtomContainerBondPermutor permutor = new AtomContainerBondPermutor(container);
* while (permutor.hasNext()) {
* IAtomContainer permutedContainer = permutor.next();
* ...
* }</pre>
*
*@author steinbeck
*
* @author maclean
* @cdk.githash
*@cdk.created 2005-05-04
*@cdk.keyword permutation
* @cdk.created 2009-09-09
* @cdk.keyword permutation
* @cdk.module standard
*/
public class AtomContainerBondPermutor extends AtomContainerPermutor
{
public class AtomContainerBondPermutor extends AtomContainerPermutor {

public AtomContainerBondPermutor(IAtomContainer ac)
{
setAtomContainer(ac);
N = atomContainer.getBondCount();
initBookkeeping();
initObjectArray();
/**
* A permutor wraps the original atom container, and produces cloned
* (and permuted!) copies on demand.
*
* @param atomContainer
*/
public AtomContainerBondPermutor(IAtomContainer atomContainer) {
super(atomContainer.getBondCount(), atomContainer);
}

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().newInstance(IAtomContainer.class,atomContainer);
ac.setBonds(bonds);
IAtomContainer clone = null;
/* (non-Javadoc)
* @see org.openscience.cdk.graph.AtomContainerPermutor#containerFromPermutation(int[])
*/
public IAtomContainer containerFromPermutation(int[] permutation) {
try {
clone = (IAtomContainer)ac.clone();
} catch (CloneNotSupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
IAtomContainer permutedContainer =
(IAtomContainer) super.atomContainer.clone();
int n = permutedContainer.getBondCount();
IBond[] permutedBonds = new IBond[n];
for (int i = 0; i < n; i++) {
permutedBonds[i] = permutedContainer.getBond(permutation[i]);
}
permutedContainer.setBonds(permutedBonds);
return permutedContainer;
} catch (CloneNotSupportedException cne) {
return null;
}
return clone;
}

}
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