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Open Source Chemistry Library
/*
* 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.
*
* @author Modest v. Korff
*/
package com.actelion.research.chem.descriptor;
import com.actelion.research.calc.Logarithm;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.datamodel.IntVec;
/**
* DescriptorHandlerBinarySkelSpheres
*
* This descriptor is a binary representation of the Skeleton Spheres descriptor. The correlation with the
* SkeletonSpheres descriptor was calculated with R²=0.9891. Basis for the correlation were one million similartiy values
* calculated from 1000 RND samples from
* /home/korffmo1/Projects/Software/Development/VirtualScreening/data/CalibrationDataset/gpcr_ligandsAllDescriptors.dwar
* the fraction of 0.25 of the highest similarity values was used to calculate the Pearson correlation coefficient.
*
* Created by korffmo1 on 09.05.17.
*
*/
public class DescriptorHandlerBinarySkelSpheres extends AbstractDescriptorHandlerFP {
public static final String VERSION = DescriptorConstants.DESCRIPTOR_BINARY_SKELETONSPHERES.version;
//
// Parameter for standardization.
//
// Widens the distribution
private static final double FAC_WIDTH = 8;
// Moves the distribution along the axis.
private static final double OFFSET_MOVE = 0.5;
// Centers the distribution around 0.
private static final double OFFSET_CENTER = 0.2;
private static DescriptorHandlerBinarySkelSpheres DEFAULT_INSTANCE;
private DescriptorHandlerSkeletonSpheres dhSkeletonSpheres;
public DescriptorHandlerBinarySkelSpheres() {
dhSkeletonSpheres = new DescriptorHandlerSkeletonSpheres();
}
@Override
public DescriptorInfo getInfo() {
return DescriptorConstants.DESCRIPTOR_BINARY_SKELETONSPHERES;
}
@Override
public String getVersion() {
return VERSION;
}
@Override
public int [] createDescriptor(StereoMolecule mol) {
byte [] arrSkelSpheres = dhSkeletonSpheres.createDescriptor(mol);
return createDescriptorFromSkelSpheresArrayCompressed(arrSkelSpheres);
}
/**
* Calculates a binary vector with half number of bits as fields in the original SkeletonSpheres descriptor.
* Th length is 512 bits.
* Two fields of the original SkeletonSpheres descriptor are summarized.
*
* @param arrSkelSpheres
* @return
*/
public static int [] createDescriptorFromSkelSpheresArrayCompressed(byte [] arrSkelSpheres) {
final int thresh = 8;
if ((arrSkelSpheres == null) || (arrSkelSpheres.length==0)){
return null;
}
final int numInteger = arrSkelSpheres.length / (Integer.SIZE * 2);
final int lenInBit = arrSkelSpheres.length / 2;
IntVec iv = new IntVec(numInteger);
for (int i = 0; i < arrSkelSpheres.length; i+=2) {
int freq = arrSkelSpheres[i] + arrSkelSpheres[i+1];
if(freq>0) {
// int bitsSet = Logarithm.log2(freq)+1;
// int bitsSet = freq;
int bitsSet = 0;
if(freq > thresh){
bitsSet = thresh+Logarithm.log2(freq-thresh)+1;
} else {
bitsSet = freq;
}
for (int j = 0; j < bitsSet; j++) {
int index= (i / 2) + j;
// int indexCircular = getCircularIndexOffset(index, lenInBit);
int indexCircular = getCircularIndexOffset(index, lenInBit);
iv.setBit(indexCircular);
}
}
}
return iv.get();
}
private static int getCircularIndexOffset(int index, int lenDescriptor){
int indexNew = index;
if(indexNew < lenDescriptor){
return indexNew;
}
indexNew = index-lenDescriptor;
return indexNew;
}
@Override
public DescriptorHandler getThreadSafeCopy() {
return new DescriptorHandlerBinarySkelSpheres();
}
/**
* Calculates the similarity by the number of common bits devided by the total number of bts.
* @param a1
* @param a2
* @return normalized similarity.
*/
@Override
public float getSimilarity(int [] a1, int [] a2){
int bcAND=0;
int bcOR=0;
for (int i = 0; i < a1.length; i++) {
final int v1 = a1[i];
final int v2 = a2[i];
bcAND += Integer.bitCount(v1 & v2);
bcOR += Integer.bitCount(v1 | v2);
}
// System.out.println("bcAND " + bcAND);
// System.out.println("bcOR " + bcOR);
double score = (double)bcAND/((double)bcOR);
// double score = (double)bcAND/((bcAND * 0.5) + (bcOR * 0.5));
// return (float)score;
return (float)correctionTS(score);
}
public static DescriptorHandlerBinarySkelSpheres getDefaultInstance() {
synchronized(DescriptorHandlerBinarySkelSpheres.class) {
if (DEFAULT_INSTANCE == null)
DEFAULT_INSTANCE = new DescriptorHandlerBinarySkelSpheres();
}
return DEFAULT_INSTANCE;
}
/**
* The parameter were derived from one million similarity scores with
* com.actelion.research.chem.descriptor.util.SimilarityCalibration
* and
* com.actelion.research.chem.descriptor.util.CalculateStandardsationFactorFromSimilarityMatrix
*
* @param s
* @return
*/
public static double standardize(double s){
if(s <= 0){
return 0;
} else if(s>=1.0){
return 1.0;
}
final double sc = s-OFFSET_CENTER;
double v = Math.exp(-FAC_WIDTH * (sc)) - OFFSET_MOVE;
return v;
}
public static double correctionTS(double s){
// double t1 = 0.615;
// double t2 = 0.615;
double t1 = 0.7;
double t2 = 0.7;
double v = 1.0-Math.pow(1-Math.pow(s, t1) ,1.0/t2);
if(v <= 0){
return 0;
} else if(v>=1.0){
return 1.0;
}
return v;
}
// public static double correctionTS(double s){
//
// double t1 = 0.5;
// double t2 = 0.8;
//
// double v = 1.0-Math.pow(1-Math.pow(s-0.2, t1) ,1.0/t2) + 0.4;
//
// if(v <= 0){
// return 0;
// } else if(v>=1.0){
// return 1.0;
// }
//
// return v;
//
// }
}