content: package com.actelion.research.chem.mcs;
  
  import java.util.ArrayList;
  import java.util.List;
  
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  
  /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its contributors may be used to endorse or promote products
  *    derived from this software without specific prior written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  */
  public class MCSFunctions {
  
  	private MCS mcs;
  
  	/**
  	 * 
  	 */
  	public MCSFunctions() {
  		mcs = new MCS();
  
  	}
  	
  	public StereoMolecule getRemainingStructure(StereoMolecule molProduct, StereoMolecule molEduct1){
  		
  		boolean [] arrBondProduct = new boolean [molProduct.getBonds()];
  		
  		boolean [] arrBondReactant2 = null;
  		
  		mcs.set(molProduct, molEduct1);
  				
  		mcs.getMCSBondArray(arrBondProduct, arrBondReactant2);
  		
  		StereoMolecule molRemainingSubstituent = new StereoMolecule(molProduct);
  				
  		molRemainingSubstituent.ensureHelperArrays(Molecule.cHelperRings);
  				
  		boolean [] arrBondProductInverse = new boolean [molProduct.getBonds()];
  		
  		for (int i = 0; i < arrBondProduct.length; i++) {
  			
  			if(!arrBondProduct[i]){
  				arrBondProductInverse[i]=true;
  			}
  		}
  		
  		molProduct.copyMoleculeByBonds(molRemainingSubstituent, arrBondProductInverse, true, null);
  		
  		molRemainingSubstituent.ensureHelperArrays(Molecule.cHelperRings);
  				
  		return molRemainingSubstituent;
  		
  	}
  	
  	public StereoMolecule getMaximumCommonSubstructure(List<StereoMolecule> li) throws Exception {
  		
  		StereoMolecule molMCS = li.get(0);
  		
  		List<StereoMolecule> liMCS = new ArrayList<StereoMolecule>();
  		
  		liMCS.add(molMCS);
  				
  		for (int i = 1; i < li.size(); i++) {
  			
  			StereoMolecule mol = li.get(i);
  			
  			mcs.set(mol, molMCS);
  			
  			molMCS = mcs.getMCS();
  			
  			if(molMCS==null){
  				System.err.println("No common substructure found. break!");
  			}
  		}
  				
  		return molMCS;
  		
  	}
  	
  	public double getScore(StereoMolecule mol, StereoMolecule frag){
  		
  		mcs.set(mol, frag);
  		
  		if(mcs.getMCS()==null){
  			return 0;
  		}
  		
  		return mcs.getScore();
  		
  	}
  
  
  
  }
  