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Open Source Chemistry Library
package com.actelion.research.chem.mcs;
import java.util.ArrayList;
import java.util.List;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.RingCollection;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.properties.complexity.IBitArray;
import com.actelion.research.chem.shredder.Fragment;
/*
* 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 BondVector2IdCode {
private StereoMolecule mol;
private List liRingSets;
public BondVector2IdCode(StereoMolecule mol) {
this.mol = mol;
liRingSets = new ArrayList();
RingCollection rc = mol.getRingSet();
int rings = rc.getSize();
for (int i = 0; i < rings; i++) {
int [] arrIndexBnd = rc.getRingBonds(i);
liRingSets.add(arrIndexBnd);
}
}
/**
*
* @param fragDefByBonds
* @return true if the fragment contains parts of a ring.
*/
public boolean containsFragmentOpenRing(IBitArray fragDefByBonds){
boolean openRing = false;
for(int [] arrIndexBnd : liRingSets){
int ccOverlap=0;
for (int i = 0; i < arrIndexBnd.length; i++) {
if(fragDefByBonds.isBitSet(arrIndexBnd[i])){
ccOverlap++;
}
}
if((ccOverlap > 0) && ccOverlap < arrIndexBnd.length) {
openRing = true;
break;
}
}
return openRing;
}
public String getFragmentIdCode(IBitArray fragDefByBonds){
StereoMolecule frag = convert(fragDefByBonds, false);
Canonizer can = new Canonizer(frag);
String idcode = can.getIDCode();
return idcode;
}
public Fragment getFragment(IBitArray fragDefByBonds){
StereoMolecule frag = convert(fragDefByBonds, false);
Canonizer can = new Canonizer(frag);
String idcode = can.getIDCode();
Fragment fragment = new Fragment(idcode);
fragment.setMol(frag);
fragment.setSize(frag.getBonds());
return fragment;
}
public Fragment getFragment(IBitArray fragDefByBonds, boolean addWildcards){
StereoMolecule frag = convert(fragDefByBonds, addWildcards);
Canonizer can = new Canonizer(frag);
String idcode = can.getIDCode();
Fragment fragment = new Fragment(idcode);
fragment.setMol(frag);
fragment.setSize(frag.getBonds());
return fragment;
}
private StereoMolecule convert(IBitArray fragDefByBonds, boolean addWildcards){
int bonds = mol.getBonds();
int atoms = mol.getAtoms();
boolean [] arrBonds = new boolean [bonds];
boolean [] arrAtoms = new boolean [atoms];
int bondsFragment = 0;
for (int i = 0; i < bonds; i++) {
if(fragDefByBonds.isBitSet(i)){
arrBonds[i] = true;
bondsFragment++;
arrAtoms[mol.getBondAtom(0, i)] = true;
arrAtoms[mol.getBondAtom(1, i)] = true;
}
}
int atomsFrag = 0;
for (int i = 0; i < arrAtoms.length; i++) {
if(arrAtoms[i]){
atomsFrag++;
}
}
StereoMolecule fragSubBonds = new StereoMolecule(atomsFrag, bondsFragment);
int [] indexAtoms = mol.copyMoleculeByBonds(fragSubBonds, arrBonds, true, null);
// Add ring and aromatic info.
// Added 07.07.2014
//
int indexAtomNew = 0;
for (int i = 0; i < indexAtoms.length; i++) {
if(indexAtoms[i]>-1) {
if((mol.getAtomQueryFeatures(indexAtoms[i]) & Molecule.cAtomQFNotChain) > 0){
fragSubBonds.setAtomQueryFeature(indexAtomNew, Molecule.cAtomQFNotChain, true);
}
if((mol.getAtomQueryFeatures(indexAtoms[i]) & Molecule.cAtomQFAromatic) > 0){
fragSubBonds.setAtomQueryFeature(indexAtomNew, Molecule.cAtomQFAromatic, true);
}
indexAtomNew++;
}
}
if(addWildcards) {
boolean [] arrAtomCopied2Fragment = new boolean [mol.getAtoms()];
for (int i = 0; i < indexAtoms.length; i++) {
if(indexAtoms[i] > -1)
arrAtomCopied2Fragment[i] = true;
}
for (int i = 0; i < indexAtoms.length; i++) {
if(indexAtoms[i] > -1) {
int atIndexOld = i;
int nConnected = mol.getConnAtoms(atIndexOld);
for (int j = 0; j < nConnected; j++) {
int indexAtConn = mol.getConnAtom(atIndexOld, j);
if(!arrAtomCopied2Fragment[indexAtConn]){
int atWildCard = fragSubBonds.addAtom(0);
int atIndexNew = indexAtoms[i];
fragSubBonds.addBond(atIndexNew, atWildCard, Molecule.cBondTypeSingle);
fragSubBonds.setAtomQueryFeature(atWildCard, Molecule.cAtomQFAny, true);
}
}
}
}
}
fragSubBonds.ensureHelperArrays(Molecule.cHelperRings);
return fragSubBonds;
}
public String getFragmentIdCodeCarbonSkeleton(IBitArray fragDefByBonds){
StereoMolecule frag = convert(fragDefByBonds, false);
for (int i = 0; i < frag.getAtoms(); i++) {
frag.setAtomicNo(i, 6);
}
Canonizer can = new Canonizer(frag);
String idcode = can.getIDCode();
return idcode;
}
}