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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.
*
*/
package com.actelion.research.chem.reaction;
import com.actelion.research.chem.SSSearcher;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.mcs.MCS;
public class CommonSubGraphHelper
{
static class Result
{
private StereoMolecule molecule;
private int reactant;
private int product;
public Result(StereoMolecule m, int rI, int pI)
{
setMolecule(m);
setReactant(rI);
setProduct(pI);
}
public String toString()
{
return "MCS Result: R=" + getReactant() + " P=" + getProduct() + " #Atoms=" + getMolecule().getAllAtoms();
}
public StereoMolecule getMolecule()
{
return molecule;
}
public void setMolecule(StereoMolecule molecule)
{
this.molecule = molecule;
}
public int getReactant()
{
return reactant;
}
public void setReactant(int reactant)
{
this.reactant = reactant;
}
public int getProduct()
{
return product;
}
public void setProduct(int product)
{
this.product = product;
}
}
// public static String findMCS(String rxnctab)
// {
// RXNFileParser p = new RXNFileParser();
// Reaction reaction = new Reaction();
// try {
// p.parse(reaction,rxnctab);
// MCS mcs = new MCS(MCS.PAR_KEEP_AROMATIC_RINGS);
// StereoMolecule a = reaction.getReactant(0);
// StereoMolecule b = reaction.getProduct(0);
// mcs.set(a,b);
// StereoMolecule m = mcs.getMCS();
// MolfileV3Creator creator = new MolfileV3Creator(m);
// return creator.getMolfile();
// } catch (Exception e) {
// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
// }
// return null;
// }
//
// public static String findMCS(Reaction reaction)
// {
// RXNFileParser p = new RXNFileParser();
// try {
// MCS mcs = new MCS(MCS.PAR_KEEP_AROMATIC_RINGS);
// StereoMolecule a = reaction.getReactant(0);
// StereoMolecule b = reaction.getProduct(0);
// mcs.set(a,b);
// StereoMolecule m = mcs.getMCS();
// MolfileV3Creator creator = new MolfileV3Creator(m);
// return creator.getMolfile();
// } catch (Exception e) {
// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
// }
// return null;
// }
public static Result getMCS(Reaction reaction, boolean[] exclude, SSSearcher sss)
{
// MCS mcs = new MCS(MCS.PAR_KEEP_RINGS,sss);
MCS mcs = new MCS(MCS.PAR_CLEAVE_RINGS,sss);
return getCommonSubGraph(mcs, reaction, exclude);
}
private static Result getCommonSubGraph(MCS mcs, Reaction reaction, boolean[] exclude)
{
Result ret = null;
try {
int rn = reaction.getReactants();
int pn = reaction.getProducts();
StereoMolecule res = null;
int resReactantIndex = -1;
int resProductIndex = -1;
int max = 0;
// Look for the biggest overlap
for (int r = 0; r < rn; r++) {
StereoMolecule reactant = reaction.getReactant(r);
for (int p = 0; p < pn; p++) {
StereoMolecule product = reaction.getProduct(p);
mcs.set(product, reactant, exclude);
StereoMolecule m = mcs.getMCS();
if (m != null) {
int na = m.getAllAtoms();
if (max < na) {
res = m;
resReactantIndex = r;
resProductIndex = p;
max = na;
// System.out.printf("Reactant %d -> Product %d max = %d\n",r,p,max);
}
}
}
}
// for (int r = rn-1; r >= 0 ; r--) {
// StereoMolecule reactant = reaction.getReactant(r);
// for (int p = 0; p < pn ; p++) {
// StereoMolecule product = reaction.getProduct(p);
// mcs.set(product, reactant, null);
// StereoMolecule m = mcs.getMCS();
// if (m != null) {
// int na = m.getAllAtoms();
// if (max < na) {
// res = m;
// resReactantIndex = r;
// resProductIndex = p;
// max = na;
// }
// }
// }
// }
if (res != null) {
//return new MCSResult(res,resReactantIndex,resProductIndex);
ret = new Result(res, resReactantIndex, resProductIndex);
}
} catch (Exception e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
return ret;
}
// public static Result[] getMCS2(Reaction rxn)
// {
// Reaction reaction = new Reaction(rxn);
// MCS mcs = new MCS(MCS.PAR_KEEP_AROMATIC_RINGS);
// Result res = getCommonSubGraph(mcs, reaction);
// remove(reaction, res.getMolecule(), res.getReactant(), res.getProduct());
// Result res2 = getCommonSubGraph(mcs, reaction);
//
// return new Result[]{
// res,
// res2
// };
// }
/* private static void remove(Reaction rxn, StereoMolecule fragment, int rIndex, int pIndex)
{
SSSearcher searcher = new SSSearcher();
StereoMolecule reactant = rxn.getReactant(rIndex);
StereoMolecule product = rxn.getProduct(pIndex);
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) {
int count = matchList.get(0).length;
// 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) {
int[] matching = matchList.get(0);
{
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]);
}
}
}
rxn.removeEmptyMolecules();
} */
}