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.StereoMolecule;
  
  public class DescriptorHandlerLongPFP512 extends AbstractDescriptorHandlerLongFP<StereoMolecule> implements DescriptorConstants {
      private static final double CORRECTION_FACTOR = 0.85;
  
      private static DescriptorHandlerLongPFP512 sDefaultInstance;
  
  	public static DescriptorHandlerLongPFP512 getDefaultInstance() {
  		synchronized (DescriptorHandlerLongPFP512.class) {
  			if (sDefaultInstance == null) {
  				sDefaultInstance = new DescriptorHandlerLongPFP512();
  			}
  		}
  		return sDefaultInstance;
  	}
  
  	public DescriptorInfo getInfo() {
  		return DESCRIPTOR_PFP512;
  	}
  
  	public String getVersion() {
  		return DescriptorConstants.DESCRIPTOR_PFP512.version;
  	}
  
  	public long[] createDescriptor(StereoMolecule mol) {
  		if (mol ==null)
  			return null;
  
  		java.util.BitSet bitset = new FingerPrintGenerator().getFingerprint(mol);
  
  		if (bitset == null)
  			return FAILED_OBJECT;
  
  		// Since reverse and vertical bits were used in the first place,
  		// we need to use his strange bit placement to keep the long version
  		// of the descriptor compatible with the encoded 32-bit version.
  		long[] fp = new long[8];
  		long mask1 = 0x0000000000000001L;
  		long mask2 = 0x0000000100000000L;
  		for (int i=0; i<32; i++) {
  			for (int j=0; j<8; j++) {
  				if (bitset.get(16 * i + 2 * j + 1))
  					fp[j] += mask1;
  				if (bitset.get(16 * i + 2 * j))
  					fp[j] += mask2;
  				}
  			mask1 <<= 1;
  			mask2 <<= 1;
  		}
  
  		return fp;
  	}
  
  	public DescriptorHandler<long[], StereoMolecule> getThreadSafeCopy() {
  		return this;
  	}
  
  	@Override
      public float getSimilarity(long[] o1, long[] o2) {
  		return normalizeValue(super.getSimilarity(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));
  	}
  }
  