content: /*
  * 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.
  *
  */
  
  package com.actelion.research.chem.properties.complexity;
  
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  
  public class SymmetryCalculator {
  	
  	/**
  	 * 
  	 */
  	public static double getRatioSymmetricAtoms(StereoMolecule mol) {
  		
  		mol.ensureHelperArrays(Molecule.cHelperNeighbours);
  		
  		// Only the biggest fragment remains
  		mol.stripSmallFragments();
  		
  		mol.ensureHelperArrays(Molecule.cHelperSymmetrySimple);
  				
  		int nAtms = mol.getAtoms();
  		
  		int maxRank = 0;
  		for (int i = 0; i < nAtms; i++) {
  			int rank = mol.getSymmetryRank(i);
  			
  			if(rank > maxRank){
  				maxRank=rank;
  			}
  		}
  		
  		
  		int nSymmetricAtms = nAtms-maxRank;
  
  		double ratio = nSymmetricAtms / (double)nAtms;
  		
  		return ratio;
  		
  	}
  
  }
  