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.util.BurtleHasher;
  
  import java.nio.charset.StandardCharsets;
  import java.util.Arrays;
  
  public class DescriptorHandlerSkeletonSpheres implements DescriptorHandler<byte[], StereoMolecule> {
      private static final double CORRECTION_FACTOR = 0.7;
  
      private static final byte[] FAILED_OBJECT = new byte[0];
      private static final int MAX_SPHERE_COUNT = 5;
      private static final int EXACT_SPHERE_COUNT = 4;
      private static final int SKELETON_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 DescriptorHandlerSkeletonSpheres sDefaultInstance;
  
      public static DescriptorHandlerSkeletonSpheres getDefaultInstance() {
      	synchronized(DescriptorHandlerSkeletonSpheres.class) {
      		if (sDefaultInstance == null) {
          		sDefaultInstance = new DescriptorHandlerSkeletonSpheres();
          		}
          	}
          return sDefaultInstance;
      	}
  
      public boolean calculationFailed(byte[] o) {
          return o==null || o.length == 0;
          }
  
      /**
       * 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 byte[] 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];
  
  //System.out.println("descriptor skeleton spheres:");
          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<MAX_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]) {
  	                            atomMask[connAtom] = true;
  	                            atomList[newMax++] = connAtom;
  	                            }
  	                        }
  	                    }
  	                min = max;
  	                max = newMax;
              		}
  
                  mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
  
                  // take fragment as it is
                  if (sphere < EXACT_SPHERE_COUNT) {
                      String idcode = new Canonizer(fragment).getIDCode();
                      int h = BurtleHasher.hashlittle(idcode, HASH_INIT);
                      h = (h & BurtleHasher.hashmask(HASH_BITS));
                      if (descriptor[h] < DescriptorEncoder.MAX_COUNT_VALUE)
                      	descriptor[h]++;
  //System.out.println("atom:"+rootAtom+"\tfragment\tradius:"+sphere+"\thash:"+h+"\t"+idcode);
                      }
  
                  // take atomic no reduced fragment skeleton also
                  if (sphere < SKELETON_SPHERE_COUNT) {
                      for (int atom=0; atom<fragment.getAllAtoms(); atom++)
                          fragment.setAtomicNo(atom, 6);
                      String idcode = new Canonizer(fragment).getIDCode();
                      int h = BurtleHasher.hashlittle(idcode, HASH_INIT);
                      h = (h & BurtleHasher.hashmask(HASH_BITS));
                      if (descriptor[h] < DescriptorEncoder.MAX_COUNT_VALUE)
                      	descriptor[h]++;
  //System.out.println("atom:"+rootAtom+"\tskeleton\tradius:"+sphere+"\thash:"+h+"\t"+idcode);
                      }
                  }
              }
  
          return descriptor;
          }
  
      public byte[] decode(String s) {
          return s == null ?               null
               : s.equals(FAILED_STRING) ? FAILED_OBJECT
               :                           new DescriptorEncoder().decodeCounts(s);
          }
  
      public byte[] decode(byte[] bytes) {
          return bytes == null ?               		null
               : Arrays.equals(bytes, FAILED_BYTES) ? FAILED_OBJECT
               :                           			new DescriptorEncoder().decodeCounts(bytes);
          }
  
      public String encode(byte[] o) {
          return calculationFailed(o) ? FAILED_STRING
               : new String(new DescriptorEncoder().encodeCounts(o), StandardCharsets.UTF_8);
          }
  
      public DescriptorInfo getInfo() {
          return DescriptorConstants.DESCRIPTOR_SkeletonSpheres;
          }
  
      public String getVersion() {
          return DescriptorConstants.DESCRIPTOR_SkeletonSpheres.version;
          }
  
      public float getSimilarity(final byte[] d1, final byte[] d2) {
          if (d1 == null || d2 == null)
              return Float.NaN;
  
          int total = 0;
          int matching = 0;
          for (int i=0; i<d1.length; i++) {
  
              final byte i1 = d1[i];
              final byte i2 = d2[i];
  
              total += Math.max(i1, i2);
              matching += Math.min(i1, i2);
              }
  /*
  if (((double)matching/(double)total) > 0.8) {
      System.out.print("i:");
      for (int i=0; i<d1.length; i++)
          if (d1[i] != d2[i])
              System.out.print(" "+i);
      System.out.println();
      System.out.print("d1:");
      for (int i=0; i<d1.length; i++)
          if (d1[i] != d2[i])
              System.out.print(" "+d1[i]);
      System.out.println();
      System.out.print("d2:");
      for (int i=0; i<d2.length; i++)
          if (d1[i] != d2[i])
              System.out.print(" "+d2[i]);
      System.out.println();
      }
  */        
          return normalizeValue((double)matching/(double)total);
          }
  
  	public 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<byte[], StereoMolecule> getThreadSafeCopy() {
  		return this;
      	}
  	}
  