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MCSPlus.java
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MCSPlus.java
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/* Copyright (C) 2006-2010 Syed Asad Rahman <asad@ebi.ac.uk>
*
* 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.smsd.algorithm.mcsplus;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Stack;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.smsd.algorithm.mcgregor.McGregor;
import org.openscience.cdk.smsd.global.TimeOut;
import org.openscience.cdk.smsd.tools.TimeManager;
/**
* This class handles MCS plus algorithm which is a combination of
* c-clique algorithm and McGregor algorithm.
* @cdk.module smsd
* @cdk.githash
* @author Syed Asad Rahman <asad@ebi.ac.uk>
*/
public class MCSPlus {
/**
* Default constructor added
*/
public MCSPlus() {
}
private static TimeManager timeManager = null;
/**
* @return the timeout
*/
protected synchronized static double getTimeout() {
return TimeOut.getInstance().getTimeOut();
}
/**
* @return the timeManager
*/
protected synchronized static TimeManager getTimeManager() {
return timeManager;
}
/**
* @param aTimeManager the timeManager to set
*/
protected synchronized static void setTimeManager(TimeManager aTimeManager) {
TimeOut.getInstance().setTimeOutFlag(false);
timeManager = aTimeManager;
}
/**
*
* @param ac1
* @param ac2
* @param shouldMatchBonds
* @return
* @throws CDKException
*/
protected List<List<Integer>> getOverlaps(IAtomContainer ac1, IAtomContainer ac2, boolean shouldMatchBonds)
throws CDKException {
Stack<List<Integer>> maxCliqueSet = null;
List<List<Integer>> mappings = new ArrayList<List<Integer>>();
try {
GenerateCompatibilityGraph gcg = new GenerateCompatibilityGraph(ac1, ac2, shouldMatchBonds);
List<Integer> compGraphNodes = gcg.getCompGraphNodes();
List<Integer> cEdges = gcg.getCEgdes();
List<Integer> dEdges = gcg.getDEgdes();
// System.err.println("**************************************************");
// System.err.println("CEdges: " + CEdges.size());
// System.out.println("DEdges: " + DEdges.size());
BKKCKCF init = new BKKCKCF(compGraphNodes, cEdges, dEdges);
maxCliqueSet = init.getMaxCliqueSet();
// System.err.println("**************************************************");
// System.err.println("Max_Cliques_Set: " + maxCliqueSet.size());
// System.out.println("Best Clique Size: " + init.getBestCliqueSize());
//clear all the compatibility graph content
gcg.clear();
while (!maxCliqueSet.empty()) {
List<Integer> cliqueList = maxCliqueSet.peek();
int cliqueSize = cliqueList.size();
if (cliqueSize < ac1.getAtomCount() && cliqueSize < ac2.getAtomCount()) {
McGregor mgit = new McGregor(ac1, ac2, mappings, shouldMatchBonds);
mgit.startMcGregorIteration(mgit.getMCSSize(), cliqueList, compGraphNodes);
mappings = mgit.getMappings();
mgit = null;
} else {
mappings = ExactMapping.extractMapping(mappings, compGraphNodes, cliqueList);
}
maxCliqueSet.pop();
if (isTimeOut()) {
break;
}
}
} catch (IOException ex) {
Logger.getLogger(MCSPlus.class.getName()).log(Level.SEVERE, null, ex);
}
return mappings;
}
public synchronized static boolean isTimeOut() {
if (getTimeout() > -1 && getTimeManager().getElapsedTimeInMinutes() > getTimeout()) {
TimeOut.getInstance().setTimeOutFlag(true);
return true;
}
return false;
}
}