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.
   *
   * @author Joel Wahl
   */
  
  package com.actelion.research.chem.conf;
  
  import com.actelion.research.chem.Coordinates;
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm;
  import com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator;
  
  import java.util.*;
  
  /**
   * employing RMSD calculation using a HungarianAlgorithm for the atom assignment to correct
   * for overestimated RMSD values obtained by conventional methods for molecules with symmetric substructures 
   * based on: dx.doi.org/10.1021/ci400534h
   *
   */
  
  public class SymmetryCorrectedRMSDCalculator {
  	private Conformer conf1;
  	private Conformer conf2;
  
  	
  	public SymmetryCorrectedRMSDCalculator(Conformer conf1, Conformer conf2) {
  		this.conf1 = conf1;
  		this.conf2 = conf2;
  	}
  	
  	public double calculate() {
  		int[][] assignments = getAssignments();
  		double rmsd = 0.0;
  		for(int[] pair : assignments) { 
  			Coordinates c1 = conf1.getCoordinates(pair[0]);
  			Coordinates c2 = conf2.getCoordinates(pair[1]);
  			rmsd+=c1.distanceSquared(c2);
  		}
  		rmsd/=assignments.length;
  		rmsd = Math.sqrt(rmsd);
  		
  		return rmsd;
  	}
  	
  	/**
  	 * using a HungarianAlgorithm for the optimal assignment of atoms for the RMSD calculation
  	 * Restriction: Only atoms having the same atom type can be assigned to each other
  	 * Cost matrix: squared distance between the atoms
  	 * @return
  	 */
  	
  	private int[][] getAssignments() {
  		List<int[]> assignments = new ArrayList<>();
  		StereoMolecule mol1 = new StereoMolecule(conf1.getMolecule());
  		StereoMolecule mol2 = new StereoMolecule(conf2.getMolecule());
  
  		mol1.ensureHelperArrays(Molecule.cHelperParities);
  		mol2.ensureHelperArrays(Molecule.cHelperParities);
  		
  		Integer[] atomTypes1 = getAtomTypes(mol1);
  		Integer[] atomTypes2 = getAtomTypes(mol2);
  	
  		Set<Integer> uniqueAtomTypes1 = new HashSet<>();
  		Collections.addAll(uniqueAtomTypes1, atomTypes1);
  		Set<Integer> uniqueAtomTypes2 = new HashSet<>();
  		Collections.addAll(uniqueAtomTypes2, atomTypes2);
  		assert(uniqueAtomTypes1.equals(uniqueAtomTypes2));
  		for(int at : uniqueAtomTypes1) { 
  			List<Integer> occurences1 = new ArrayList<>();
  			List<Integer> occurences2 = new ArrayList<>();
  			for(int i=0;i<atomTypes1.length;i++) {
  				int at1 = atomTypes1[i];
  				if(at1==at)
  					occurences1.add(i);
  			}
  			for(int i=0;i<atomTypes2.length;i++) {
  				int at2 = atomTypes2[i];
  				if(at2==at)
  					occurences2.add(i);
  			}
  			assert(occurences1.size()==occurences2.size());
  			double[][] costMatrix = new double[occurences1.size()][occurences2.size()];
  			int counter1 = 0;
  			for(int occ1 : occurences1) { 
  				int counter2 = 0;
  				for(int occ2 : occurences2) {
  					double distSq = conf1.getCoordinates(occ1).distanceSquared(conf2.getCoordinates(occ2));
  					costMatrix[counter1][counter2] = distSq;
  					counter2++;
  				}
  				counter1++;
  			}
  			int[][] ass = HungarianAlgorithm.hgAlgorithm(costMatrix, "min");
  			for(int[] pair : ass) {
  				int p1 = occurences1.get(pair[0]);
  				int p2 = occurences2.get(pair[1]);
  				assignments.add(new int[] {p1,p2});
  			}
   		}
  		return assignments.toArray(new int[assignments.size()][2]);
  		
  	}
  	
  	private Integer[] getAtomTypes(StereoMolecule mol) {
  		Integer[] atomTypes = new Integer[mol.getAtoms()];
  		for(int a=0;a<mol.getAtoms();a++) {
  			atomTypes[a] = InteractionAtomTypeCalculator.getAtomType(mol, a);
  		}
  		return atomTypes;
  	}
  	
  	
  	
  
  }
  