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Open Source Chemistry Library
package com.actelion.research.chem.mcs;
import java.util.Date;
import java.util.List;
import com.actelion.research.chem.ExtendedMolecule;
import com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions;
import com.actelion.research.chem.properties.complexity.IBitArray;
import com.actelion.research.util.Formatter;
import com.actelion.research.util.SizeOf;
import com.actelion.research.util.datamodel.IntArray;
/*
* 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.
*
*/
public class ExhaustiveFragmentGeneratorBonds {
private static boolean ELUSIVE = false;
public static final long LIMIT_NEIGHBOURS_SINCE_LAST_ADDED = 100 * 1000 * 1000;
// This list contains the solutions. Each row in the list contains the solutions for the corresponding number of atom types.
// Consequently, the first two rows are empty.
private ContainerFragBondsSolutions containerDataFragDefByBonds;
private ExtendedMolecule mol;
private int nBondsMolecule;
private int maximumNumberBondsInFrag;
private IntArray arrIndexReachableNeighbours;
private boolean fragmentsGenerated;
private boolean capacityLimitBreakes;
private long solutionAdded;
private int totalMaximumCapacity;
/**
* @param bits maximum fragment size that can be stored as number of bonds.
*/
public ExhaustiveFragmentGeneratorBonds(int bits, int totalMaximumCapacity) {
ContainerFragBondsSolutions.ELUSIVE = ELUSIVE;
this.totalMaximumCapacity = totalMaximumCapacity;
containerDataFragDefByBonds = new ContainerFragBondsSolutions(bits, totalMaximumCapacity);
arrIndexReachableNeighbours = new IntArray();
if(ELUSIVE)
System.out.println("ExhaustiveFragmentGeneratorBonds constructor finished, used mem " + SizeOf.usedMemoryMB() + "[MB].");
}
public void set(ExtendedMolecule mol, int nMaximumNumberBonds) {
this.mol = mol;
nBondsMolecule = mol.getBonds();
if(nBondsMolecule > containerDataFragDefByBonds.getSizeBinaryArray()){
throw new RuntimeException("Maximum number of bonds exceeded.");
}
this.maximumNumberBondsInFrag = Math.min(nMaximumNumberBonds, containerDataFragDefByBonds.getMaximumCapacityBondsInFragment());
fragmentsGenerated = false;
capacityLimitBreakes=false;
containerDataFragDefByBonds.setBondsMolecule(nBondsMolecule);
}
private void initDataContainerAllSingleBonds(){
containerDataFragDefByBonds.reset();
for (int i = 0; i < nBondsMolecule; i++) {
IBitArray f = containerDataFragDefByBonds.get();
f.setBit(i);
containerDataFragDefByBonds.addFacultative(f);
}
}
private void initDataContainerOneSingleBond(int indexBond) {
containerDataFragDefByBonds.reset();
IBitArray f = containerDataFragDefByBonds.get();
f.setBit(indexBond);
containerDataFragDefByBonds.addFacultative(f);
}
public void generateFragmentsAllBonds(){
initDataContainerAllSingleBonds();
generateFragments();
}
public void generateFragmentsForSingleBond(int indexBond) {
initDataContainerOneSingleBond(indexBond);
generateFragments();
}
private void generateFragments(){
int maxNumBondsFrag = Math.min(nBondsMolecule, maximumNumberBondsInFrag);
if(maxNumBondsFrag==1){
return;
}
long neighboursTotal = 0;
long addedTotal = 0;
if(ELUSIVE) {
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() start record capacity " + Formatter.group(containerDataFragDefByBonds.getAvailable()) + ".");
}
maximumCapacityBreak:
for (int i = 1; i < maxNumBondsFrag; i++) {
List liParent = containerDataFragDefByBonds.getList(i);
if(ELUSIVE) {
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() bonds " + i + ". Parents " + Formatter.group(liParent.size()) + ".");
}
long added = 0;
long neighbours = 0;
long neighboursSinceLastAdded = 0;
for (IBitArray fParent : liParent) {
IntArray arrBondsReachable = getAllReachableNeighbourBonds(mol, fParent);
for (int j = 0; j < arrBondsReachable.length(); j++) {
IBitArray fChildAddedBond = containerDataFragDefByBonds.getWithCopy(fParent);
fChildAddedBond.setBit(arrBondsReachable.get(j));
// System.out.println(fChildAddedBond.toString());
if(containerDataFragDefByBonds.addFacultative(fChildAddedBond)){
added++;
addedTotal++;
neighboursSinceLastAdded = 0;
if(addedTotal>totalMaximumCapacity) {
if(ELUSIVE) {
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() maximum capacity (" + totalMaximumCapacity + ") break.");
log(neighbours, neighboursTotal, added, addedTotal, neighboursSinceLastAdded);
}
// Clear all records for this number of bonds.
containerDataFragDefByBonds.reset(fChildAddedBond.getBitsSet());
break maximumCapacityBreak;
}
}
neighbours++;
neighboursSinceLastAdded++;
if(neighbours % 50000000 == 0){
if(ELUSIVE) {
log(neighbours, neighboursTotal, added, addedTotal, neighboursSinceLastAdded);
}
}
}
// if(neighboursSinceLastAdded > LIMIT_NEIGHBOURS_SINCE_LAST_ADDED) {
if(neighboursSinceLastAdded > totalMaximumCapacity) {
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments(). Break for fragments with " + i + " bonds. Generated " + totalMaximumCapacity + " neighbours since last add to hash map.");
break;
}
}
// System.out.println("Bonds\t" + i + "\tparents\t" + liParent.size() + "\tneighbours added\t" + added);
neighboursTotal += neighbours;
if(ELUSIVE) {
log(neighbours, neighboursTotal, added, addedTotal, neighboursSinceLastAdded);
}
}
fragmentsGenerated = true;
if(ELUSIVE) {
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() getTotalSizeResultList() " + Formatter.group(containerDataFragDefByBonds.getTotalSizeResults()) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() solutionAdded " + Formatter.group(solutionAdded) + ".");
}
}
private void log(long neighbours, long neighboursTotal, long added, long addedTotal, long neighboursSinceLastAdded){
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() " + new Date().toString() + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() neighbours generated " + Formatter.group(neighbours) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() neighbours generated total " + Formatter.group(neighboursTotal) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() solutions added " + Formatter.group(added) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() solutions added total " + Formatter.group(addedTotal) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() available " + Formatter.group(containerDataFragDefByBonds.getAvailable()) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() capacity " + Formatter.group(containerDataFragDefByBonds.getCapacity()) + ".");
System.out.println("ExhaustiveFragmentGeneratorBonds generateFragments() neighboursSinceLastAdded " + Formatter.group(neighboursSinceLastAdded) + ".");
}
/**
* Returns list with indices for fragments with size bonds. The indices are coded as bit lists.
* @param bonds
* @return
*/
public List getFragments(int bonds) {
if(!fragmentsGenerated){
throw new RuntimeException("Fragments have to be generated first. Call generateFragments().");
}
return containerDataFragDefByBonds.getList(bonds);
}
/**
* get all bonds that can be reached in one step from the input bonds.
* @param mol
* @param livIndexBond
* @return
*/
private final IntArray getAllReachableNeighbourBonds(ExtendedMolecule mol, IBitArray livIndexBond){
arrIndexReachableNeighbours.reset();
for (int i = 0; i < nBondsMolecule; i++) {
if(!livIndexBond.isBitSet(i)){
continue;
}
final int indexBond = i;
final int indexAtom1 = mol.getBondAtom(0, indexBond);
final int indexAtom2 = mol.getBondAtom(1, indexBond);
final int nConnected1 = mol.getAllConnAtoms(indexAtom1);
for (int j = 0; j < nConnected1; j++) {
int indexAtConn = mol.getConnAtom(indexAtom1, j);
int indexBondConnected = mol.getBond(indexAtom1, indexAtConn);
if(!livIndexBond.isBitSet(indexBondConnected)) {
solutionAdded++;
arrIndexReachableNeighbours.add(indexBondConnected);
}
}
final int nConnected2 = mol.getAllConnAtoms(indexAtom2);
for (int j = 0; j < nConnected2; j++) {
int indexAtConn = mol.getConnAtom(indexAtom2, j);
int indexBondConnected = mol.getBond(indexAtom2, indexAtConn);
if(!livIndexBond.isBitSet(indexBondConnected)) {
solutionAdded++;
arrIndexReachableNeighbours.add(indexBondConnected);
}
}
}
return arrIndexReachableNeighbours;
}
/**
* If true not all index combinations were generated.
* Starts with 0 for each new molecule.
* @return
*/
public boolean isCapacityLimitBreakes() {
return capacityLimitBreakes;
}
public int getSizeArrayLIV(){
int maxSizeIntVec = (containerDataFragDefByBonds.getSizeBinaryArray() + Integer.SIZE-1)/ Integer.SIZE;
return maxSizeIntVec;
}
public int getMaximumCapacityBondsInFragment() {
return containerDataFragDefByBonds.getMaximumCapacityBondsInFragment();
}
public int getMaximumNumberBondsInMolecule(){
return containerDataFragDefByBonds.getMaximumNumberBondsInMolecule();
}
/**
* @return the eLUSIVE
*/
public static boolean isELUSIVE() {
return ELUSIVE;
}
/**
* @param elusive the ELUSIVE to set
*/
public static void setELUSIVE(boolean elusive) {
ELUSIVE = elusive;
ContainerFragBondsSolutions.ELUSIVE = ELUSIVE;
}
}