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.SSSearcherWithIndex;
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.util.BurtleHasher;
  import com.actelion.research.util.datamodel.IntVec;
  
  import java.util.Arrays;
  
  public class DescriptorHandlerHashedCFp extends AbstractDescriptorHandlerFP<StereoMolecule> {
      private static final double CORRECTION_FACTOR = 0.6;
  
      private static DescriptorHandlerHashedCFp sDefaultInstance;
      
      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);
  
      public static DescriptorHandlerHashedCFp getDefaultInstance() {
      	synchronized(DescriptorHandlerHashedCFp.class) {
      		if (sDefaultInstance == null) {
                  sDefaultInstance = new DescriptorHandlerHashedCFp();
          	}
          }
          return sDefaultInstance;
      }
  
      public DescriptorInfo getInfo() {
          return DescriptorConstants.DESCRIPTOR_HashedCFp;
      }
  
      public String getVersion() {
          return DescriptorConstants.DESCRIPTOR_HashedCFp.version;
      }
  
      /**
       * This descriptor requires proper up/down bonds, because it encodes stereo parities.
       * If a passed molecule is generated from idcode parsing, make sure that coordinates
       * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with
       * the respective option.
       */
      public int[] createDescriptor(StereoMolecule mol) {
          if (mol ==null)
              return null;
  
          mol.ensureHelperArrays(Molecule.cHelperRings);
          StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());
  
          // byte[] descriptor = new byte[DESCRIPTOR_SIZE];
          int len = DESCRIPTOR_SIZE / Integer.SIZE;
          IntVec iv = new IntVec(len); 
  
  		int[] atomList = new int[mol.getAtoms()];
          boolean[] atomMask = new boolean[mol.getAtoms()];
          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) + mol.getMetalBondedConnAtoms(atom); j++) {
                              int connAtom = mol.getConnAtom(atom, j);
                              if (!atomMask[connAtom]) {
                                  atomMask[connAtom] = true;
                                  atomList[newMax++] = connAtom;
                                  }
                              }
                          }
                      min = max;
                      max = newMax;
                      }
  
                  mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
  
                  // take fragment as it is
                  String idcode = new Canonizer(fragment).getIDCode();
                  int h = BurtleHasher.hashlittle(idcode, HASH_INIT);
                  h = (h & BurtleHasher.hashmask(HASH_BITS));
                  iv.setBit(h);
  
  //System.out.println("atom:"+rootAtom+"\tsphere:"+sphere+"\thash:"+h+"\t"+idcode);
                  }
              }
  
          return iv.get();
          }
  
      public float getSimilarity(int[] o1, int[] o2) {
          return o1 == null
              || o2 == null
              || o1.length == 0
              || o2.length == 0 ? 0.0f
          : normalizeValue(SSSearcherWithIndex.getSimilarityTanimoto(o1, o2));
      }
      
  	private float normalizeValue(double value) {
  		return value <= 0.0f ? 0.0f
  			 : value >= 1.0f ? 1.0f
  			 : (float)(1.0-Math.pow(1-Math.pow(value, CORRECTION_FACTOR) ,1.0/CORRECTION_FACTOR));
  	}
  
      public DescriptorHandler<int[], StereoMolecule> getThreadSafeCopy() {
      	return this;
      }
  
  }
  