com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule Maven / Gradle / Ivy
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package com.actelion.research.chem.properties.fractaldimension;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.properties.complexity.BitArray128;
import com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics;
import com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics;
import com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic;
import com.actelion.research.util.PointUtils;
import java.awt.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* FractalDimensionMolecule
* Modest v. Korff
*
* Created by korffmo1 on 28.08.18.
* 04.11.2021 Changed resultFracDimCalc.fractalDimension = Math.log10(nMaxFrags) / Math.log10(nBondsAtMaxNumFrag);
* into resultFracDimCalc.fractalDimension = Math.log10(nMaxFrags) / Math.log10(nBondsAtMaxNumFrags+1);
* otherwise we have a division by zero error nBondsAtMaxNumFrags=1. Resulted in infinite complexity score.
*/
public class FractalDimensionMolecule {
public static final String MSG_ZERO = "Zero by definition. Max bond count at one bond.";
private static final int MAX_THREADS_BOND_VECTOR_TO_IDCODE = 12;
private static final int BONDS_LIMIT_STATS = 18;
private ExhaustiveFragmentsStatistics exhaustiveFragmentsStatistics;
boolean elusive;
public FractalDimensionMolecule(int totalCapacity, boolean elusive) {
ExhaustiveFragmentsStatistics.setELUSIVE(elusive);
this.elusive = elusive;
// int threadsBondVector2IdCode = Runtime.getRuntime().availableProcessors()-1;
int threadsBondVector2IdCode = Math.min(MAX_THREADS_BOND_VECTOR_TO_IDCODE, Runtime.getRuntime().availableProcessors()-1);
if(threadsBondVector2IdCode==0){
threadsBondVector2IdCode=1;
}
exhaustiveFragmentsStatistics = new ExhaustiveFragmentsStatistics(BitArray128.MAX_NUM_BITS, threadsBondVector2IdCode, totalCapacity);
}
public ResultFracDimCalc process(InputObjectFracDimCalc inputObjectFracDimCalc){
ResultFracDimCalc resultFracDimCalc = new ResultFracDimCalc(inputObjectFracDimCalc);
StereoMolecule mol = inputObjectFracDimCalc.getData();
int bonds = inputObjectFracDimCalc.getData().getBonds();
if(bonds<3){
resultFracDimCalc.message = "Num bonds in molecule below limit of 3.";
return resultFracDimCalc;
} else if(bonds > exhaustiveFragmentsStatistics.getMaximumNumberBondsInMolecule()){
resultFracDimCalc.message = "Num bonds in molecule above limit of " + exhaustiveFragmentsStatistics.getMaximumNumberBondsInMolecule() + ".";
return resultFracDimCalc;
}
int maxNumBondsStats = bonds -1;
if(bonds>BONDS_LIMIT_STATS)
maxNumBondsStats = bonds - 2;
System.out.println("Process molecule " + inputObjectFracDimCalc.getId() + " with " + bonds + " bonds. maxNumBondsStats " + maxNumBondsStats + ".");
ResultFragmentsStatistic resultFragmentsStatistic = exhaustiveFragmentsStatistics.create(mol, maxNumBondsStats);
List liModelExhaustiveStatistics = resultFragmentsStatistic.getExhaustiveStatistics();
List liFragBnds_NumUniqueFrags = new ArrayList<>();
for (ModelExhaustiveStatistics modelExhaustiveStatistic : liModelExhaustiveStatistics) {
liFragBnds_NumUniqueFrags.add(new Point(modelExhaustiveStatistic.getNumBondsInFragment(), modelExhaustiveStatistic.getUnique()));
}
Collections.sort(liFragBnds_NumUniqueFrags, PointUtils.getComparatorX());
Point pBnds_MaxNumUniqueFrags = getMaxNumUniqueFrags(liFragBnds_NumUniqueFrags);
int nBondsAtMaxNumFrags = pBnds_MaxNumUniqueFrags.x;
int nMaxFrags = pBnds_MaxNumUniqueFrags.y;
if(nBondsAtMaxNumFrags==1){
resultFracDimCalc.fractalDimension = 0;
resultFracDimCalc.message = MSG_ZERO;
} else {
resultFracDimCalc.fractalDimension = Math.log10(nMaxFrags) / Math.log10(nBondsAtMaxNumFrags);
resultFracDimCalc.bondsAtMaxFrag = nBondsAtMaxNumFrags;
resultFracDimCalc.maxNumUniqueFrags = nMaxFrags;
resultFracDimCalc.sumUniqueFrags = getSumUniqueFrags(liFragBnds_NumUniqueFrags);
}
return resultFracDimCalc;
}
public void finalizeThreads() throws Throwable {
if(exhaustiveFragmentsStatistics!=null) {
exhaustiveFragmentsStatistics.roundUp();
}
}
public static int getSumUniqueFrags(List liFragBnds_NumUniqueFrags) {
int sum = 0;
int indexMaxNumUniqueFrags = getIndexMaxNumUniqueFrags(liFragBnds_NumUniqueFrags);
int end = indexMaxNumUniqueFrags+1;
for (int i = 0; i < end; i++) {
int nFragsUnique = liFragBnds_NumUniqueFrags.get(i).y;
sum += nFragsUnique;
}
return sum;
}
public static Point getMaxNumUniqueFrags(List liFragBnds_NumUniqueFrags) {
int indexMaxNumUniqueFrags = getIndexMaxNumUniqueFrags(liFragBnds_NumUniqueFrags);
return liFragBnds_NumUniqueFrags.get(indexMaxNumUniqueFrags);
}
public static int getIndexMaxNumUniqueFrags(List liFragBnds_NumUniqueFrags){
int indexMaxNumUniqueFrags = -1;
int maxNumUniqueFrags = 0;
for (int i = 0; i < liFragBnds_NumUniqueFrags.size(); i++) {
Point pFragBnds_NumUniqueFrags = liFragBnds_NumUniqueFrags.get(i);
int nUniqueFrags = pFragBnds_NumUniqueFrags.y;
if(nUniqueFrags>maxNumUniqueFrags){
maxNumUniqueFrags=nUniqueFrags;
indexMaxNumUniqueFrags=i;
}
}
return indexMaxNumUniqueFrags;
}
}