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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 Thomas Sander
*/
package com.actelion.research.chem.reaction.mapping;
import com.actelion.research.chem.StereoMolecule;
import java.util.ArrayList;
import java.util.TreeMap;
/**
* This is a helper class for the RuleEnhancedMapper, which expects most of a reaction's atoms
* to be already mapped using an MCS or similarity guided graph-matching approach.
* This class tries all permutations of unmapped reactant and product atoms provided their
* atomic numbers and atom masses match. All solutions are scored considering bonds changed
* and the best scoring solution is added to the mapping number arrays.
* This class assumes a stoichiometrical reaction and, thus, always the same number of unmapped
* reactant atoms and products atoms in the same atom class.
*/
public class ReactionCenterMapper {
private static final int MAX_PERMUTATION_COUNT = 4000000;
private ArrayList mAtomClasses;
private StereoMolecule mReactant,mProduct;
private int[] mReactantMapNo,mProductMapNo;
private int mStartMapNo,mMapNo;
public ReactionCenterMapper(StereoMolecule reactant, StereoMolecule product, int[] reactantMapNo, int[] productMapNo, int mapNo) {
mReactant = reactant;
mProduct = product;
mReactantMapNo = reactantMapNo;
mProductMapNo = productMapNo;
mStartMapNo = mapNo;
mMapNo = mapNo;
// For every atomicNo/isotop create an UnmappedCenterAtoms class with respective reactant and product atoms
TreeMap atomClassMap = new TreeMap<>();
for (int atom=0; atom();
for (UnmappedCenterAtoms uca:atomClassMap.values())
if (!uca.mapObviousAtoms())
mAtomClasses.add(uca);
}
/** Tries and scores all possible mapping permutations for all of hitherto unmapped atoms.
* The best scoring combination is kept and its score returned.
* If there are no unmapped atoms, then the score of the current mapping is returned.
*/
public float completeAndScoreMapping() {
// For efficient scoring we build a reactionAtomToProductAtom map,
// which is updated with the center atom assignments for every scoring.
MappingScorer scorer = new MappingScorer(mReactant, mProduct);
int[] reactantToProductAtom = scorer.createReactantToProductAtomMap(mReactantMapNo, mProductMapNo);
if (mAtomClasses.size() == 0)
return scorer.scoreMapping(reactantToProductAtom);
double totalPermutationCount = 1;
for (UnmappedCenterAtoms uca:mAtomClasses)
totalPermutationCount *= uca.getPermutationCount();
if (totalPermutationCount > MAX_PERMUTATION_COUNT) {
System.out.println("permutationCount exceeds maximum:"+totalPermutationCount);
return 0;
}
int atomCount = 0;
int[] cumulatedAtomCount = new int[mAtomClasses.size()];
int[] permutationCount = new int[mAtomClasses.size()];
for (int i=0; i mPermutationList;
public void addReactantAtom(int atom) {
mReactantAtom = addAtom(atom, mReactantAtom);
if (mReactantAtom.length <= mProductAtom.length)
mMappableAtomCount = mReactantAtom.length;
}
public void addProductAtom(int atom) {
mProductAtom = addAtom(atom, mProductAtom);
if (mProductAtom.length <= mReactantAtom.length)
mMappableAtomCount = mProductAtom.length;
}
/**
* If we have only one atom of this kind, or if we have all equal un-bonded atoms
* on one reaction side, then we can safely map these atoms.
* @return true if all mappable atoms were mapped
*/
public boolean mapObviousAtoms() {
if (mMappableAtomCount == 0)
return true;
if (mReactantAtom.length == 1 && mProductAtom.length == 1) {
mMapNo++;
mReactantMapNo[mReactantAtom[0]] = mMapNo;
mProductMapNo[mProductAtom[0]] = mMapNo;
return true;
}
// to qualify as equal in the context of already mapped atoms,
// atoms must not only be symmetrical, they must also not have any neighbours.
boolean reactantAtomsAreEqual = areEqualSingleAtoms(mReactantAtom, mReactant);
if (reactantAtomsAreEqual && mReactantAtom.length <= mProductAtom.length) {
for (int i=0; i= mProductAtom.length) {
for (int i=0; i(); // contains pointer array from reactant to product
int[] solution = new int[mMappableAtomCount];
boolean[] isUsed = new boolean[Math.max(mReactantAtom.length, mProductAtom.length)];
permute(0, isUsed, solution);
return mPermutationList.size();
}
private void permute(int index, boolean[] isUsed, int[] solution) {
for (int i=0; i mProductAtom.length) {
for (int i=0; i