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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
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package com.actelion.research.chem.reaction;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.SSSearcher;
import com.actelion.research.chem.StereoMolecule;
import java.util.ArrayList;
import java.util.Arrays;
public class MCSReactionMapper implements IReactionMapper
{
private static int COLORTABLE[] = {
Molecule.cAtomColorNone,
Molecule.cAtomColorBlue,
Molecule.cAtomColorRed,
Molecule.cAtomColorGreen,
Molecule.cAtomColorMagenta,
Molecule.cAtomColorOrange,
Molecule.cAtomColorDarkGreen,
};
static final int PRODUCTFLAG = 200;
static final int REACTANTFLAG_ATOMNUMBER = 105;
static final int PRODUCTFLAG_ATOMNUMBER = 106;
static final int REACTANTFLAG = 100;
private int mapIndex = 0;
private static int colorIndex = 1;
public static int getNextColor()
{
colorIndex = ++colorIndex % COLORTABLE.length;
if (colorIndex == 0)
++colorIndex;
return COLORTABLE[colorIndex];
}
public Reaction matchReaction(Reaction reaction)
{
return mapReaction(reaction,null);
}
@Override
public Reaction mapReaction(Reaction reaction, SSSearcher sss)
{
mapIndex = 0;
try {
CommonSubGraphHelper.Result mcsResult = CommonSubGraphHelper.getMCS(reaction,null,sss);
while (mcsResult != null) {
int color = getNextColor();
StereoMolecule fragment = mcsResult.getMolecule();
fragment.setFragment(true);
// Do we need this???
// CoordinateInventor coordinateInventor = new CoordinateInventor();
// coordinateInventor.invent(fragment);
StereoMolecule target = reaction.getReactant(mcsResult.getReactant());
// matchlist returns the indices on the
// A matchlist contains the the matched atom index for each atom on the target
// (Atom-) Array[0..n] (of fragment) contains indizes of the matched target atoms
// Fragment atom(f)[x] => atom(t)[matchList[x]] in target
int matchList[] = findMatches(fragment, target, sss);
if (matchList != null && matchList.length > 0) {
applyMaps(fragment, target, matchList);
// We mark temporarely the atom with an invalid atom number, so it gets excluded from the SSS in MCS
// TLS 11Feb2021: this is an awful hack that destroys atom lists in the SSS matching. We need to do that better in the new due ReactionMapper!!!
// TLS 11Feb2021: Introduced restoration of atom mass to be able to use atom mass matching by the SSSearcher
for (int i = 0; i < matchList.length; i++) {
int atom = matchList[i];
int t = REACTANTFLAG + target.getAtomicNo(atom);
target.setAtomList(atom, new int[]{t});
int atomMass = target.getAtomMass(atom); // retain original atom mass
target.setAtomicNo(atom, REACTANTFLAG_ATOMNUMBER);
target.setAtomMass(atom, atomMass);
}
target = reaction.getProduct(mcsResult.getProduct());
fragment.setFragment(true);
matchList = findMatches(fragment, target, sss);
applySourceMapOnTarget(fragment, target, matchList);
for (int i = 0; i < matchList.length; i++) {
int atom = matchList[i];
int t = PRODUCTFLAG + target.getAtomicNo(atom);
target.setAtomList(atom, new int[]{t});
int atomMass = target.getAtomMass(atom); // retain original atom mass
target.setAtomicNo(atom, PRODUCTFLAG_ATOMNUMBER);
target.setAtomMass(atom, atomMass);
}
System.out.println(mcsResult);
mcsResult = CommonSubGraphHelper.getMCS(reaction, null, sss);
} else {
// If we did not have any matches, we could not mark any atoms with dummy atom no,
// so any further attempt would lead to the same result, hence endless loop!
break;
}
}
// Reset the temporarely marked atoms
for (int i = 0; i < reaction.getMolecules(); i++) {
StereoMolecule mol = reaction.getMolecule(i);
for (int j = 0; j < mol.getAllAtoms(); j++) {
if (mol.getAtomicNo(j) == REACTANTFLAG_ATOMNUMBER) {
if(mol.getAtomList(j) != null) {
int atomMass = mol.getAtomMass(j); // retain original atom mass
mol.setAtomicNo(j, mol.getAtomList(j)[0] - REACTANTFLAG);
mol.setAtomMass(j, atomMass);
mol.setAtomList(j, null);
}
} else if (mol.getAtomicNo(j) == PRODUCTFLAG_ATOMNUMBER) {
if(mol.getAtomList(j) != null) {
int atomMass = mol.getAtomMass(j); // retain original atom mass
mol.setAtomicNo(j, mol.getAtomList(j)[0] - PRODUCTFLAG);
mol.setAtomMass(j, atomMass);
mol.setAtomList(j, null);
}
}
}
}
reaction.setFragment(false);
return reaction;
} catch (Exception e1) {
e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
return null;
}
}
public void resetFragments(Reaction rxn)
{
for (int i = 0; i < rxn.getMolecules(); i++) {
rxn.getMolecule(i).setFragment(false);
}
}
public void removeMapping(Reaction reaction)
{
for (int i = 0; i < reaction.getMolecules(); i++) {
StereoMolecule mol = reaction.getMolecule(i);
for (int j = 0; j < mol.getAllAtoms(); j++) {
mol.setAtomMapNo(j, 0, false);
}
}
}
private int[] findMatches(StereoMolecule fragment, StereoMolecule molecule, SSSearcher searcher)
{
searcher.setMol(fragment, molecule); // fragment, molecule
int a = searcher.findFragmentInMolecule(SSSearcher.cCountModeOverlapping, SSSearcher.cDefaultMatchMode);
ArrayList matchList = searcher.getMatchList(); // found match list of target
if (matchList != null && matchList.size() != 0) {
return matchList.get(0);
}
return null;
}
private int[] highlightQuery(StereoMolecule fragment, StereoMolecule molecule, int color,SSSearcher searcher)
{
searcher.setMol(fragment, molecule); // fragment, molecule
int a = searcher.findFragmentInMolecule(SSSearcher.cCountModeOverlapping, SSSearcher.cDefaultMatchMode);
ArrayList matchList = searcher.getMatchList(); // found match list of target
if (matchList != null && matchList.size() != 0) {
for (int[] matching : matchList) {
for (int k = 0; k < matching.length; k++) {
molecule.setAtomColor(matching[k], color);
}
}
return matchList.get(0);
}
return null;
}
private void applyMaps(StereoMolecule fragment, StereoMolecule molecule, int matchList[])
{
for (int atom = 0; atom < matchList.length; atom++) {
fragment.setAtomMapNo(atom, ++mapIndex, true);
molecule.setAtomMapNo(matchList[atom], mapIndex, true);
}
}
private void applySourceMapOnTarget(StereoMolecule source, StereoMolecule target, int matchList[])
{
for (int atom = 0; atom < matchList.length; atom++) {
int map = source.getAtomMapNo(atom);
target.setAtomMapNo(matchList[atom], map, true);
}
}
private boolean validateMapping(Reaction reaction)
{
int reactants = reaction.getReactants();
int products = reaction.getProducts();
int[][] rMaps = new int[reactants][];
int[][] pMaps = new int[products][];
for (int r = 0; r < reactants; r++) {
StereoMolecule src = reaction.getReactant(r);
rMaps[r] = getMappingNos(src);
}
for (int p = 0; p < products; p++) {
StereoMolecule target = reaction.getProduct(p);
pMaps[p] = getMappingNos(target);
}
if (!matchMappings(rMaps, pMaps))
return false;
return true;
}
private boolean matchMappings(int[][] rMaps, int[][] pMaps)
{
for (int i = 0; i < rMaps.length; i++) {
for (int sourceMapNo : rMaps[i]) {
if (sourceMapNo == 0)
continue;
boolean found = false;
for (int j = 0; j < pMaps.length; j++) {
for (int targetMapNo : pMaps[j]) {
if (sourceMapNo == targetMapNo)
found = true;
}
}
if (!found)
return false;
}
}
return true;
}
private int[] getMappingNos(StereoMolecule molecule)
{
int ret[] = new int[molecule.getAllAtoms()];
int atoms = molecule.getAllAtoms();
for (int atom = 0; atom < atoms; atom++) {
ret[atoms] = molecule.getAtomMapNo(atom);
}
return ret;
}
private void remove(StereoMolecule fragment, StereoMolecule reactant, StereoMolecule product)
{
SSSearcher searcher = new SSSearcher();
StereoMolecule candidates[] = {
reactant,
product
};
for (StereoMolecule candidate : candidates) {
searcher.setMol(fragment, candidate);
searcher.findFragmentInMolecule(SSSearcher.cCountModeOverlapping, SSSearcher.cDefaultMatchMode);
ArrayList matchList = searcher.getMatchList();
if (matchList != null && matchList.size() != 0) {
int count = 0;
for (int[] matching : matchList) {
for (int k = 0; k < matching.length; k++) {
count++;
}
}
int remove[] = new int[count];
int idx = 0;
for (int[] matching : matchList) {
for (int k = 0; k < matching.length; k++) {
remove[idx++] = matching[k];
}
}
Arrays.sort(remove);
for (int i = remove.length - 1; i >= 0; i--) {
candidate.deleteAtom(remove[i]);
}
}
}
}
}