com.actelion.research.chem.descriptor.flexophore.DistHist Maven / Gradle / Ivy
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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.calc.ArrayUtilsCalc;
import com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class DistHist implements Serializable {
private static final long serialVersionUID = 17042013;
// Array containing the histogram vectors.
// Only one array, because of memory reasons.
protected byte [] arrDistHists;
private int numPPNodes;
private int identifier;
public DistHist() {
arrDistHists = new byte[0];
numPPNodes = 0;
identifier=-1;
}
/**
* Initializes the distance histograms. Filled with 0.
* @param nPPNodes
*/
public DistHist(int nPPNodes) {
initHistogramArray(nPPNodes);
}
public DistHist(DistHist distHist) {
distHist.copy(this);
}
/**
*
* @param copy: This object is written into copy.
*/
public void copy(DistHist copy){
copy.identifier = this.identifier;
if(copy.numPPNodes != this.numPPNodes) {
copy.numPPNodes = this.numPPNodes;
copy.arrDistHists = new byte[this.arrDistHists.length];
}
System.arraycopy(this.arrDistHists, 0, copy.arrDistHists, 0, this.arrDistHists.length);
}
public int getBonds() {
return ((numPPNodes * numPPNodes)-numPPNodes) / 2;
}
/**
*
* @return number of pharmacophore points.
*/
public int getNumPPNodes(){
return numPPNodes;
}
public int getSizeBytes(){
int s = 0;
if(getNumPPNodes()>1) {
s += arrDistHists.length;
}
// size, identifier
s += (Integer.SIZE / 8)*2;
return s;
}
protected void initHistogramArray(int nPPNodes) {
this.numPPNodes = nPPNodes;
int nBonds = ((numPPNodes * numPPNodes)-numPPNodes) / 2;
arrDistHists = new byte[nBonds* ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
}
/**
*
* @param indexNode1
* @param indexNode2
* @param size number of nodes
* @return
*/
public static final int getIndex(int indexNode1, int indexNode2, int size){
int i1 = Math.min(indexNode1,indexNode2);
int i2 = Math.max(indexNode1,indexNode2);
int h = i1+1;
int index = (i1*size+i2) - ((h*h-h)/2) - h;
return index;
}
public int getMinDist(int indexAt1, int indexAt2) {
byte [] arr = getDistHist(indexAt1, indexAt2);
int dist=0;
for (int i = 0; i < arr.length; i++) {
if(arr[i]>0){
dist = i;
break;
}
}
return dist;
}
/**
* Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
* @param maxDistance maximum distance that a node will become a cluster member
* @return List with cluster.
*/
public List getClusterCenter(int maxDistance){
List liCluster = new ArrayList();
// Get all cluster
for (int i = 0; i < getNumPPNodes(); i++) {
ClusterNode cluster = new ClusterNode(i);
for (int j = 0; j < getNumPPNodes(); j++) {
if(i!=j){
byte [] hist = getDistHist(i, j);
boolean bInCluster=false;
for (int k = 0; k < maxDistance+1; k++) {
if(hist[k]>0){
bInCluster=true;
break;
}
}
if(bInCluster){
cluster.add(j);
}
}
}
if(cluster.isCluster())
liCluster.add(cluster);
}
// Calculate RMSD
for (int i = 0; i < liCluster.size(); i++) {
ClusterNode cl = liCluster.get(i);
int rmsd = ClusterNode.getRMSD(cl, this);
cl.setRMSD(rmsd);
}
// Equal cluster into one list
// The cluster with the lowest rmsd is the chosen cluster center.
List liClusterNodeMinRMSD = new ArrayList();
for (int i = 0; i < liCluster.size()-1; i++) {
ClusterNode cl = liCluster.get(i);
List liEqCluster = new ArrayList();
liEqCluster.add(cl);
for (int j = liCluster.size()-1; j > i; j--) {
if(cl.equals(liCluster.get(j))){
liEqCluster.add(liCluster.remove(j));
}
}
Collections.sort(liEqCluster);
liClusterNodeMinRMSD.add(liEqCluster.get(0));
}
return liClusterNodeMinRMSD;
}
/**
* The distance histograms are stored in a single array.
* @param indexAt1
* @param indexAt2
* @param arrHist a deep copy is taken.
*/
public void setDistHist(int indexAt1, int indexAt2, byte [] arrHist) {
if(indexAt1 >= numPPNodes) {
throw new ArrayIndexOutOfBoundsException(indexAt1);
} else if(indexAt2 >= numPPNodes)
throw new ArrayIndexOutOfBoundsException(indexAt2);
int index = getIndex(indexAt1, indexAt2, numPPNodes);
int posStart = index * ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
System.arraycopy(arrHist, 0, arrDistHists, posStart, ConstantsFlexophoreGenerator.BINS_HISTOGRAM);
}
public byte [] getDistHists() {
return arrDistHists;
}
/**
* Flat copy
* @param arr
* @param size
* @param identifier
*/
public void setDistHists(byte [] arr, int size, int identifier) {
arrDistHists=arr;
this.numPPNodes = size;
this.identifier = identifier;
}
/**
*
* @param indexAt1
* @param indexAt2
* @return deep copy.
*/
public byte [] getDistHist(int indexAt1, int indexAt2) {
int index = getIndex(indexAt1, indexAt2, numPPNodes);
int posStart = index * ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
byte [] arr = new byte[ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
System.arraycopy(arrDistHists, posStart, arr, 0, ConstantsFlexophoreGenerator.BINS_HISTOGRAM);
return arr;
}
public int getIndexPosStartForDistHist(int indexAt1, int indexAt2) {
int index = getIndex(indexAt1, indexAt2, numPPNodes);
int posStart = index * ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
return posStart;
}
public byte getValueAtAbsolutePosition(int indexAbsolutePosition){
return arrDistHists[indexAbsolutePosition];
}
public byte [] getDistHist(int indexAt1, int indexAt2, byte [] arr) {
int index = getIndex(indexAt1, indexAt2, numPPNodes);
int posStart = index * ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
System.arraycopy(arrDistHists, posStart, arr, 0, ConstantsFlexophoreGenerator.BINS_HISTOGRAM);
return arr;
}
/**
* To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
* @param indexAt1
* @param indexAt2
* @return relative distance 0: only the first bin is occupied,
* 1: the last bin is occupied.
*/
public double getRelMaxDistInHist(int indexAt1, int indexAt2) {
byte [] arr = getDistHist(indexAt1, indexAt2);
double max = Integer.MIN_VALUE;
for (int i = arr.length-1; i >= 0; i--) {
if(arr[i]>0){
max = i;
break;
}
}
return max / arr.length;
}
public double getMaxDistInHist(int indexAt1, int indexAt2) {
byte [] arr = getDistHist(indexAt1, indexAt2);
double max = Integer.MIN_VALUE;
for (int i = arr.length-1; i >= 0; i--) {
if(arr[i]>0){
max = i;
break;
}
}
return max;
}
/**
* To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
* Maximum relative distance between two nodes in the object.
* @return
*/
public double getRelMaxDistInHist() {
int size = getNumPPNodes();
double max = 0;
for (int i = 0; i < size; i++) {
for (int j = i+1; j < size; j++) {
double dist = getRelMaxDistInHist(i, j);
if(dist>max)
max=dist;
}
}
return max;
}
public String toStringHistsIndexed(){
StringBuffer b = new StringBuffer();
for (int i = 0; i < numPPNodes; i++) {
for (int j = i+1; j < numPPNodes; j++) {
byte [] arrHist = getDistHist(i,j);
if(arrHist!=null)
b.append(i + "\t" + j + "\t[" + ArrayUtilsCalc.toString(arrHist) + "]\n");
}
}
return b.toString();
}
public int getIdentifier() {
return identifier;
}
public void setIdentifier(int identifier) {
this.identifier = identifier;
}
}