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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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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
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package com.actelion.research.chem.reaction;
import java.util.ArrayList;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.coords.CoordinateInventor;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.SSSearcher;
import com.actelion.research.chem.SortedStringList;
import com.actelion.research.chem.StereoMolecule;
public class Reactor {
private Reaction mGenericReaction;
private SSSearcher mSSSearcher;
private StereoMolecule[] mReactant;
private int[][] mMinFreeValence; // minimum required free valence on reactant atoms
private boolean[][] mIsReactionCenter; // reaction center flags on product atoms
private boolean mRetainCoordinates,mFullyMapReactions,mUniqueProductsOnly;
private int mMaxGenericMapNo,mMaxCount,mReactantMatchCombinationCount;
private ArrayList[] mMatchList;
private int[][][] mReactantMapNo; // Reactant mapNos of the real reactant change with every reactant substructure match
private StereoMolecule[][] mProduct;
private String[][] mIDCode;
private boolean[] mIsDuplicate;
/**
* Constructs a Reactor that is able to construct products from a generic reaction (transformation)
* and a list of real world reactants. Reactors built with this constructor will not use product
* atom coordinates from the generic products, nor will they be able to generate fully mapped reactions.
* They will produce and return all unique products or reactions.
* @param reaction generic reactions consisting of reactant substructures with optional query features
*/
public Reactor(Reaction reaction) {
this(reaction, false, false, Integer.MAX_VALUE, true);
}
/**
* Constructs a Reactor that is able to construct products from a generic reaction (transformation)
* and a list of real world reactants. Reactors built with this constructor will be able to generate
* fully mapped reactions, They will produce and return all unique products or reactions.
* @param reaction generic reactions consisting of reactant substructures with optional query features
* @param retainCoordinates if true, then atom coordinates from the generic products are taken into the real world products
*/
public Reactor(Reaction reaction, boolean retainCoordinates) {
this(reaction, retainCoordinates, false, Integer.MAX_VALUE, true);
}
/**
* Constructs a Reactor that is able to construct products from a generic reaction (transformation)
* and a list of real world reactants. The reactor may or may not use atoms coordinates from the generic
* products, when generating clean product atom coordinates.
* @param reaction generic reactions consisting of reactant substructures with optional query features
* @param retainCoordinates if true, then atom coordinates from the generic products are taken into the real world products
* @param fullyMapReactions if true, then real world reactants and products will have valid mapping numbers after product generation
* @param maxProducts maximum number of products/reactions to be enumerated
* @param uniqueOnly whether to skip duplicate products/reactions because of starting material symmetry
*/
public Reactor(Reaction reaction, boolean retainCoordinates, boolean fullyMapReactions, int maxProducts, boolean uniqueOnly) {
// If retainCoordinates is true, then the relative orientation of the
// generic product's atom coordinates are retained in the real products.
mGenericReaction = reaction;
mRetainCoordinates = retainCoordinates;
mFullyMapReactions = fullyMapReactions;
mReactant = new StereoMolecule[reaction.getReactants()];
mMaxCount = maxProducts;
mUniqueProductsOnly = uniqueOnly;
// for sub-structure-search all generic reactants must be fragments
for (int i=0; i 0) ? dif : 0;
}
}
}
}
}
}
// mark all reaction center atoms in product
mIsReactionCenter = new boolean[reaction.getProducts()][];
for (int i=0; i neighbourMapNo) {
minNeighbourMapNo = neighbourMapNo;
minNeighbourIndex = n;
}
}
}
neighbourHandled[minNeighbourIndex] = true;
pruductNeighbours <<= 10;
pruductNeighbours += minNeighbourMapNo;
}
// get sorted list of mapping no's of attached atoms in reactant
long reactantNeighbours = 0;
neighbourHandled = new boolean[reactant.getConnAtoms(l)];
for (int m=0; m neighbourMapNo) {
minNeighbourMapNo = neighbourMapNo;
minNeighbourIndex = n;
}
}
}
neighbourHandled[minNeighbourIndex] = true;
reactantNeighbours <<= 10;
reactantNeighbours += minNeighbourMapNo;
}
if (pruductNeighbours != reactantNeighbours)
mIsReactionCenter[i][j] = true;
}
}
}
}
}
}
mSSSearcher = new SSSearcher();
mMatchList = new ArrayList[mReactant.length];
}
/**
* Removes unmatched mapping numbers and mapping numbers on exclude atoms
* @param rxn
*/
private void removeMappingErrors(Reaction rxn) {
mMaxGenericMapNo = 0;
for (int i=0; i();
mReactantMatchCombinationCount = 0;
return;
}
// eliminate matches where reaction would exceed an atom valence
mMatchList[no] = mSSSearcher.getMatchList();
for (int j=mMatchList[no].size()-1; j>=0; j--) {
int[] matchingAtom = mMatchList[no].get(j);
for (int k=0; k 0
&& mMinFreeValence[no][k] > mReactant[no].getFreeValence(matchingAtom[k])) {
mMatchList[no].remove(j);
break;
}
}
}
}
mReactantMatchCombinationCount = 1;
for (int i=0; i 0 && count > mMaxCount)
count = mMaxCount;
return count;
}
/**
* After instantiating the Reactor with fullyMappedReaction==true and after supplying real reactants,
* this method may be used to construct the fully mapped reaction. If one or more reactants have multiple
* matches of their generic reactants, then multiple reactions leading to isomeric products are returned.
* After calling this method, one or more new real reactants may provided with setReactant()
* before calling this method again.
* @return array with one or more reactions
*/
public Reaction[] getFullyMappedReactions() {
ensureProducts();
Reaction[] reaction = new Reaction[getProductCount()];
int count = 0;
int index = 0;
int[] matchIndex = new int[mReactant.length];
do {
if (!mIsDuplicate[index] || !mUniqueProductsOnly) {
reaction[count] = new Reaction();
for (int i=0; i[] matchList, int[] matchListIndex, int genericProductNo) {
// currently only support for first product of generic reaction
StereoMolecule genericProduct = mGenericReaction.getProduct(genericProductNo);
StereoMolecule product = new StereoMolecule();
int esrGroupCountAND = 0;
int esrGroupCountOR = 0;
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy