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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.flexophore;
import com.actelion.research.chem.descriptor.DescriptorEncoder;
import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
import com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator;
import com.actelion.research.util.datamodel.IntVec;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
public class DistHistEncoder {
private static DistHistEncoder INSTANCE;
private int iNBitsEntriesCountOneHistogram;
private int iNBitsPos;
private int iNBitsConsequentEntries;
private int iNBitsCountOneField;
/**
*
*/
public DistHistEncoder() {
init();
}
private void init(){
int iNumConf = DescriptorHandlerFlexophore.NUM_CONFORMATIONS;
int iLenHist = ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
//
// So many bits are needed to describe the number of fields > 0 in one histogram.
//
int maxNumEntriesOneHist = ConstantsFlexophoreGenerator.BINS_HISTOGRAM / 2;
iNBitsEntriesCountOneHistogram = 1;
while(Math.pow(2,iNBitsEntriesCountOneHistogram) < maxNumEntriesOneHist){
iNBitsEntriesCountOneHistogram++;
}
iNBitsConsequentEntries = iNBitsEntriesCountOneHistogram;
//
// So many bits are needed to describe the position of one entry in a histogram.
//
iNBitsPos = 1;
while(Math.pow(2,iNBitsPos)0)
iOccupied++;
}
nApproxBitsNeeded += iNBitsEntriesCountOneHistogram + iOccupied * (iNBitsPos + iNBitsCountOneField + iNBitsConsequentEntries);
}
}
boolean [] arr = new boolean [nApproxBitsNeeded];
int posArray=0;
for (int i = 0; i < numPPNodes; i++) {
for (int j = i+1; j < numPPNodes; j++) {
byte [] arrHist = dh.getDistHist(i,j);
int nFieldsOccupied = 0;
for (int k = 0; k < arrHist.length; k++) {
if(arrHist[k]>0)
nFieldsOccupied++;
}
// Set number of entries for histogram.
for (int k = 0; k < iNBitsEntriesCountOneHistogram; k++) {
if((nFieldsOccupied&1)==1){
arr[posArray]=true;
}
nFieldsOccupied >>>= 1;
posArray++;
}
boolean histogramProcessed = false;
int k = 0;
while(!histogramProcessed){
if(arrHist[k] > 0) {
int posInHist = k;
// Encode position
for (int l = 0; l < iNBitsPos; l++) {
if((posInHist&1)==1){
arr[posArray]=true;
}
posInHist >>>= 1;
posArray++;
}
int nConsequentFieldsOcc=1;
for (int l = k+1; l < arrHist.length; l++) {
if(arrHist[l] > 0) {
nConsequentFieldsOcc++;
} else {
break;
}
}
int nConsequentFieldsOcc2Bit = nConsequentFieldsOcc;
for (int m = 0; m < iNBitsConsequentEntries; m++) {
if((nConsequentFieldsOcc2Bit & 1)==1){
arr[posArray]=true;
}
nConsequentFieldsOcc2Bit >>>= 1;
posArray++;
}
int startSet = k;
int endSet = k+nConsequentFieldsOcc;
for (int l = startSet; l < endSet; l++) {
int counts = arrHist[l];
for (int m = 0; m < iNBitsCountOneField; m++) {
if((counts & 1)==1){
arr[posArray]=true;
}
counts >>>= 1;
posArray++;
}
}
k += nConsequentFieldsOcc;
}
// If the last field in the histogram is occupied k becomes here 40.
// The next field would be 41.
k++;
if(k >= arrHist.length){
histogramProcessed=true;
}
}
}
}
boolean [] arrTruncated = new boolean [posArray];
System.arraycopy(arr, 0, arrTruncated, 0, arrTruncated.length);
IntVec iv = new IntVec(arrTruncated);
String s = new String(new DescriptorEncoder().encode(iv.get()), StandardCharsets.UTF_8);
return s;
}
public void decodeHistograms(String s, MolDistHist mdh){
IntVec iv = new IntVec(new DescriptorEncoder().decode(s));
List liHist = new ArrayList();
boolean decodeFinished=false;
int pos = 0;
while(!decodeFinished){
int nEntriesInHistogram = getDecodedValue(iv, pos, iNBitsEntriesCountOneHistogram);
if(nEntriesInHistogram==0){
break;
}
pos += iNBitsEntriesCountOneHistogram;
byte[] arrHist = new byte [ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
int processedEntries = 0;
while(processedEntries != nEntriesInHistogram){
int positionField = getDecodedValue(iv, pos, iNBitsPos);
pos += iNBitsPos;
int consequentCounts = getDecodedValue(iv, pos, iNBitsConsequentEntries);
pos += iNBitsConsequentEntries;
for (int j = 0; j < consequentCounts; j++) {
int counts = getDecodedValue(iv, pos, iNBitsCountOneField);
pos += iNBitsCountOneField;
arrHist[positionField++]=(byte)counts;
}
processedEntries += consequentCounts;
}
liHist.add(arrHist);
if(pos+iNBitsEntriesCountOneHistogram >= iv.sizeBits()){
break;
}
}
int size = getNumNodes(liHist.size());
if(size==0){
throw new RuntimeException("Number of pharmacophore points is 0.");
}
int cc=0;
for (int i = 0; i < size; i++) {
for (int j = i+1; j < size; j++) {
mdh.setDistHist(i,j, liHist.get(cc++));
}
}
}
private static int getNumNodes(int nHistogramms){
int nNodes = 0;
int cc=0;
while(cc <= nHistogramms){
nNodes++;
cc += nNodes;
}
return nNodes;
}
private static int getDecodedValue(IntVec iv, int posStart, int widthInBits){
int posEnd = posStart + widthInBits;
int value = 0;
// The first bit is the lowest.
for (int i = posEnd-1; i >= posStart; i--) {
value <<=1;
if(iv.isBitSet(i)){
value |= 1;
}
}
return value;
}
public static DistHistEncoder getInstance(){
if(INSTANCE == null){
INSTANCE = new DistHistEncoder();
}
return INSTANCE;
}
}