com.actelion.research.chem.descriptor.flexophore.DistHistHelper Maven / Gradle / Ivy
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/*
* 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.calc.statistics.median.ModelMedianInteger;
import com.actelion.research.util.datamodel.IntArray;
/**
* DistHistHelper
* Modest v. Korff
*
* Created by korffmo1 on 13.10.20.
*/
public class DistHistHelper {
public static int getSpread(byte [] a){
int start=0;
for (int i = 0; i < a.length; i++) {
if(a[i]>0){
start=i;
break;
}
}
int end=0;
for (int i = a.length-1; i >= 0; i--) {
if(a[i]>0){
end=i;
break;
}
}
return end-start+1;
}
public static int getMaxIndexNotZero(byte [] a){
int end=0;
for (int i = a.length-1; i >= 0; i--) {
if(a[i]>0){
end=i;
break;
}
}
return end;
}
public static int getMedianBin(byte [] a){
int medianBin=-1;
int sum = 0;
for (byte b : a) {
sum+=b;
}
sum /= 2;
int s2=0;
for (int i = 0; i < a.length; i++) {
s2+=a[i];
if(s2>=sum){
medianBin=i;
break;
}
}
return medianBin;
}
public static RangeStatistics getRangeStatistics(MolDistHist mdh){
RangeStatistics rangeStatisticsTotal = new RangeStatistics();
int n = mdh.getNumPPNodes();
int nn = ((n*n)-n)/2;
IntArray iaMaxRange = new IntArray(nn);
IntArray iaMedianRange = new IntArray(nn);
for (int i = 0; i < n; i++) {
for (int j = i+1; j < n; j++) {
byte [] arr = mdh.getDistHist(i, j);
int indexMax = -1;
for (int k = arr.length-1; k >= 0; k--) {
if(arr[k]>0){
indexMax = k;
break;
}
}
iaMaxRange.add(indexMax);
int indexMin = -1;
for (int k = 0; k < arr.length; k++) {
if(arr[k]>0){
indexMin = k;
break;
}
}
int sum=0;
for (int k = indexMin; k < indexMax+1; k++) {
sum += arr[k];
}
int half = sum / 2;
sum=0;
int indexMedian1=-1;
for (int k = indexMin; k < indexMax+1; k++) {
sum += arr[k];
if(sum>=half){
indexMedian1=k;
break;
}
}
sum=0;
int indexMedian2=-1;
for (int k = indexMax; k >= indexMin; k--) {
sum += arr[k];
if(sum>=half){
indexMedian2=k;
break;
}
}
int medianRange = (int)((indexMedian1+indexMedian2)/2.0 +0.5);
iaMedianRange.add(medianRange);
}
}
ModelMedianInteger mmi = ArrayUtilsCalc.getMedian(iaMedianRange.get());
rangeStatisticsTotal.maxRange = iaMaxRange.max();
rangeStatisticsTotal.medianRange = mmi.median;
return rangeStatisticsTotal;
}
public static class RangeStatistics {
public int maxRange;
public int medianRange;
}
}