content: package com.actelion.research.chem.phesa.pharmacophore.pp;
  
  import java.util.ArrayList;
  import java.util.List;
  
  import com.actelion.research.chem.Coordinates;
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.util.ArrayUtils;
  
  public class AromRingPoint implements IPharmacophorePoint {
  	private int referenceAtom;
  	private List<Integer> ringAtoms;
  	private Coordinates center;
  	private static final Coordinates directionality = new Coordinates(1.0,0.0,0.0);
  
  	/**
  	 *
  	 * @param mol
  	 * @param a is included in ringAtoms
  	 * @param ringAtoms
  	 */
  	public AromRingPoint(StereoMolecule mol, int a, List<Integer> ringAtoms) {
  		referenceAtom = a;
  		this.ringAtoms = ringAtoms;
  		updateCoordinates(mol.getAtomCoordinates());
  	}
  	
  	public AromRingPoint(AromRingPoint aP) {
  		referenceAtom = aP.referenceAtom;
  		center = new Coordinates(aP.center);
  		ringAtoms = new ArrayList<Integer>();
  		for(int ringAtom : aP.ringAtoms) {
  			ringAtoms.add(ringAtom);
  		}
  	}
  
  	@Override
  	public Coordinates getCenter() {
  		return center;
  	}
  
  	@Override
  	public void updateCoordinates(Coordinates[] coords) {
  		Coordinates com = new Coordinates(0,0,0);
  		for(int ringAtom : ringAtoms) {
  			com.add(coords[ringAtom]);
  		}
  		com.scale(1.0/( ringAtoms.size()));
  
  		center = com;
  	}
  	
  
  	
  
  	@Override
  	public Coordinates getDirectionality() {
  		// TODO Auto-generated method stub
  		return directionality;
  	}
  	
  	private AromRingPoint(String ppString, StereoMolecule mol) {
  		decode(ppString,mol);
  	}
  	
  	public static AromRingPoint fromString(String ppString, StereoMolecule mol) {
  		return new AromRingPoint(ppString,mol);
  	}
  	
  
  	private void decode(String ppString, StereoMolecule mol) {
  		String[] strings = ppString.split(" ");
  		referenceAtom = Integer.decode(strings[1]);
  		ringAtoms = new ArrayList<Integer>();
  		for(int i=2;i<strings.length;i++) {
  			ringAtoms.add(Integer.decode(strings[i]));
  		}
  		updateCoordinates(mol.getAtomCoordinates());
  	}
  
  	@Override
  	public String encode() {
  		StringBuilder molVolString = new StringBuilder();
  		molVolString.append("r");
  		molVolString.append(" ");
  		molVolString.append(Integer.toString(referenceAtom));
  		molVolString.append(" ");
  		//molVolString.append(Integer.toString(neighbours.size()));
  		//molVolString.append(" ");
  		for(Integer ringAtom : ringAtoms) {
  			molVolString.append(ringAtom);
  			molVolString.append(" ");
  		}
  		return molVolString.toString().trim();
  	}
  
  	@Override
  	public double getSimilarity(IPharmacophorePoint pp) {
  		double result = 0.0;
  		if(pp instanceof AromRingPoint) {
  			result = 1.0;
  		}
  		return result;
  	}
  
  	@Override
  	public int getCenterID() {
  		return referenceAtom;
  	}
  	
  	@Override
  	public void setCenterID(int centerID) {
  		referenceAtom = centerID;
  	}
  
  	@Override
  	public void setDirectionality(Coordinates directionality) {
  		return;
  
  	}
  	
  
  	@Override
  	public void updateAtomIndices(int[] map) {
  		referenceAtom = map[referenceAtom];
  		for(int i=0;i<ringAtoms.size();i++) {
  			int neighbour = map[ringAtoms.get(i)];
  			ringAtoms.set(i, neighbour);
  		}
  	}
  
  	@Override
  	public int[] getAtomIndices() {
  		return ArrayUtils.toIntArray(ringAtoms);
  	}
  
  	@Override
  	public IPharmacophorePoint copyPharmacophorePoint() {
  		// TODO Auto-generated method stub
  		return new AromRingPoint(this);
  	}
  
  	@Override
  	public void getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim) {
  		return; //no directionality 
  		
  	}
  	
  	@Override 
  	
  	public double getVectorSimilarity(IPharmacophorePoint pp2,Coordinates directionalityMod) {
  		return 1.0;
  	}
  		
  	@Override
  	 public double getVectorSimilarity(IPharmacophorePoint pp2) {
  		return 1.0;
  	}
  	
  	@Override
  	public int getFunctionalityIndex() {
  		return Functionality.AROM_RING.getIndex();
  	}
  
  	@Override
  	public Coordinates getRotatedDirectionality(double[][] rotMatrix,double scaleFactor) {
  		Coordinates directMod = new Coordinates(directionality);
  		return directMod;
  	}
  
  
  }
  