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.descriptor;
  
  import com.actelion.research.chem.Canonizer;
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.chem.reaction.Reaction;
  import com.actelion.research.util.BurtleHasher;
  
  import java.util.Arrays;
  
  public class DescriptorHandlerReactionFP extends AbstractDescriptorHandlerLongFP<Reaction> {
  	public static final String cVersion = "1.0.0";
  
  	public static final int REACTION_CENTER_LONG_COUNT = 8;
  	public static final float REACTION_CENTER_WEIGHT = 0.8f;	// the percentage of reaction center similarity to contribute to the total similarity
  	public static final float PERIPHERY_WEIGHT = 1f - REACTION_CENTER_WEIGHT;
  
  	private static final int SPHERE_COUNT = 5;
  	private static final int HASH_BITS = 10;
  	private static final int HASH_INIT = 13;
  	private static final int DESCRIPTOR_SIZE = (1 << HASH_BITS);
  
      private static DescriptorHandlerReactionFP sDefaultInstance;
  
      public static DescriptorHandlerReactionFP getDefaultInstance() {
          if (sDefaultInstance == null) {
          	synchronized(DescriptorHandlerReactionFP.class) {
          		sDefaultInstance = new DescriptorHandlerReactionFP();
          	}
          }
          return sDefaultInstance;
      }
  
      public DescriptorInfo getInfo() {
          return DescriptorConstants.DESCRIPTOR_ReactionFP;
      }
  
      public String getVersion() {
          return DescriptorConstants.DESCRIPTOR_ReactionFP.version;
      }
  
      public long[] createDescriptor(Reaction rxn) {
  	    if (rxn == null)
  		    return null;
  
  	    boolean[] isReactionCenterMapNo = rxn.getReactionCenterMapNos();
  		if (isReactionCenterMapNo == null)
  			return FAILED_OBJECT;
  
  		final int len = DESCRIPTOR_SIZE / Long.SIZE;
  		long[] data = new long[len];
  
  //System.out.println("mol\tisProduct\tatom\tsphere\tisRC\thash\tindex\tbit\tidcode");
  		for (int m=0; m<rxn.getMolecules(); m++) {
  			StereoMolecule mol = rxn.getMolecule(m);
  			mol.ensureHelperArrays(Molecule.cHelperRings);
  			boolean[] isReactionCenterAtom = new boolean[mol.getAllAtoms()];
  			int reactionCenterAtomCount = rxn.getReactionCenterAtoms(m, isReactionCenterMapNo, isReactionCenterAtom, null);
  
  			StereoMolecule fragment = new StereoMolecule(mol.getAllAtoms(), mol.getAllBonds());
  
  			int[] atomList = new int[mol.getAllAtoms()];
  			boolean[] atomMask = new boolean[mol.getAllAtoms()];
  			for (int rootAtom=0; rootAtom<mol.getAtoms(); rootAtom++) {
  				if (rootAtom != 0)
  					Arrays.fill(atomMask, false);
  
  				int min = 0;
  				int max = 0;
  				for (int sphere=0; sphere<SPHERE_COUNT && max<mol.getAtoms(); sphere++) {
  					if (max == 0) {
  						atomList[0] = rootAtom;
  						atomMask[rootAtom] = true;
  						max = 1;
  						}
  					else {
  						int newMax = max;
  						for (int i=min; i<max; i++) {
  							int atom = atomList[i];
  							for (int j=0; j<mol.getConnAtoms(atom); j++) {
  								int connAtom = mol.getConnAtom(atom, j);
  								if (!atomMask[connAtom]
  								 && (isReactionCenterAtom[rootAtom] || !isReactionCenterAtom[connAtom])) {
  									atomMask[connAtom] = true;
  									atomList[newMax++] = connAtom;
  									}
  								}
  							}
  
  						if (max == newMax)
  							break;
  
  						min = max;
  						max = newMax;
  						}
  
  					mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
  
  					// take fragment as it is
  					String idcode = new Canonizer(fragment).getIDCode();
  
  					// we want product fragments to create a different set of hash codes
  					if (m >= rxn.getReactants())
  						idcode = idcode.concat("P");
  
  					// For reaction center atoms smaller fragments have higher weights, which is achieved by a higher number of representing bits
  					int weight = isReactionCenterAtom[rootAtom] ? SPHERE_COUNT - sphere : 1;
  					for (int i=0; i<weight; i++) {
  						int h = BurtleHasher.hashlittle(idcode.concat(Integer.toString(i)), HASH_INIT);
  						h = (h & BurtleHasher.hashmask(HASH_BITS-1));		// '-1' divides the full bit span into two equal parts for reaction center and non-reaction center
  
  						// we put the non-reaction-center bits at the end; high h values translate into low indexes
  						if (isReactionCenterAtom[rootAtom])
  							h += (1 << (HASH_BITS-1));
  
  						int index = len - h / Long.SIZE - 1;
  						data[index] |= (1L << (h % Long.SIZE));
  //System.out.println(""+m+"\t"+Boolean.toString(m >= rxn.getReactants())+"\t"+rootAtom+"\t"+sphere+"\t"+isReactionCenterAtom[rootAtom]+"\t"+h+"\t"+index+"\t"+(h % Long.SIZE)+"\t"+idcode);
  						}
  					}
  				}
  			}
  
  		return data;
  //		return (descriptor == null) ? FAILED_OBJECT : descriptor;
          }
  
  	public float getSimilarity(long[] o1, long[] o2) {
  		if (o1 == null
  		 || o2 == null
  		 || o1.length == 0
  		 || o2.length == 0)
  			return 0.0f;
  
  		float reactionCenterSimilarity = getSimilarityTanimoto(o1, o2, 0, REACTION_CENTER_LONG_COUNT);
  		float nonReactionCenterSimilarity = getSimilarityTanimoto(o1, o2, REACTION_CENTER_LONG_COUNT, o1.length);
  		return REACTION_CENTER_WEIGHT * reactionCenterSimilarity + PERIPHERY_WEIGHT * nonReactionCenterSimilarity;
  	}
  
  	public float getReactionCenterSimilarity(long[] o1, long[] o2) {
  		if (o1 == null
  		 || o2 == null
  		 || o1.length == 0
  		 || o2.length == 0)
  			return 0.0f;
  
  		return getSimilarityTanimoto(o1, o2, 0, REACTION_CENTER_LONG_COUNT);
  		}
  
  	public float getPeripherySimilarity(long[] o1, long[] o2) {
  		if (o1 == null
  		 || o2 == null
  		 || o1.length == 0
  		 || o2.length == 0)
  			return 0.0f;
  
  		return getSimilarityTanimoto(o1, o2, REACTION_CENTER_LONG_COUNT, o1.length);
  		}
  
  	public static float getSimilarityTanimoto(final long[] index1, final long[] index2, int i1, int i2) {
  		int sharedKeys = 0;
  		int allKeys = 0;
  		for (int i=i1; i<i2; i++) {
  			sharedKeys += Long.bitCount(index1[i] & index2[i]);
  			allKeys += Long.bitCount(index1[i] | index2[i]);
  		}
  		return allKeys == 0 ? 1f : (float)sharedKeys/(float)allKeys;
  	}
  
  	public DescriptorHandler<long[], Reaction> getThreadSafeCopy() {
  		return this;
  	}
  }
  