@@ -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"
* 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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