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MolWitch implementation that uses CDK as the underlying cheminformatics framework.
/*
* NCATS-MOLWITCH-CDK
*
* Copyright (c) 2023.
*
* This work is free software; you can redistribute it and/or modify it under the terms of the
* GNU Lesser General Public License as published by the Free Software Foundation;
* either version 2.1 of the License, or (at your option) any later version.
*
* This work is distributed in the hope that it will be useful, but without any warranty;
* without even the implied warranty of merchantability or fitness for a particular purpose.
* See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License along with this library;
* if not, write to:
*
* the Free Software Foundation, Inc.
* 59 Temple Place, Suite 330
* Boston, MA 02111-1307 USA
*/
package gov.nih.ncats.molwitch.cdk;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.BiConsumer;
import org.openscience.cdk.AtomRef;
import org.openscience.cdk.BondRef;
import org.openscience.cdk.aromaticity.Aromaticity;
import org.openscience.cdk.aromaticity.ElectronDonation;
import org.openscience.cdk.aromaticity.Kekulization;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.Cycles;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.isomorphism.matchers.Expr;
import org.openscience.cdk.isomorphism.matchers.Expr.Type;
import org.openscience.cdk.isomorphism.matchers.QueryAtom;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryBond;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smarts.Smarts;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.periodictable.PeriodicTable;
import gov.nih.ncats.molwitch.Chemical;
import gov.nih.ncats.molwitch.ChemicalSource;
public class CdkUtil {
private static final Aromaticity AROMATICITY = new Aromaticity(ElectronDonation.daylight(), Cycles.or(Cycles.all(), Cycles.all(6)));
public static void aromatize(IAtomContainer container) throws CDKException {
setImplicitHydrogensIfNeeded(container, false);
// Aromaticity.cdkLegacy().apply(container);
AROMATICITY.apply(container);
}
public static IAtomContainer safeClone(IAtomContainer iac) {
//the CDK clone doesn't actually clone deep, but still allows modifications
return (IAtomContainer)asChemical(iac).copy().getImpl().getWrappedObject();
}
public static Chemical asChemical(IAtomContainer iac) {
return new Chemical(new CdkChemicalImpl(iac,(ChemicalSource)null));
}
public static void poorMansKekulize(IAtomContainer iac) {
throw new UnsupportedOperationException("simple kekule not yet implemnted");
//basic logic:
// 1. Find all atoms with aromatic bonds
// 2. For any atom that has only 1 aromatic bond: fail
// 3. For any atom that has 2 aromatic bonds, look at H count
// and determine where double bonds could go.
// for(IBond bond : iac.bonds()){
// if(bond.isAromatic()){
//
// }
// }
}
public static IAtomContainer kekulizeIfNeeded(IAtomContainer container, boolean makeCopy) throws CDKException {
IAtomContainer possibleCopy = setImplicitHydrogensIfNeeded(container, makeCopy);
boolean setBonds=false;
for(IBond bond : possibleCopy.bonds()){
if(bond.getOrder() ==null || bond.getOrder()==Order.UNSET){
setBonds=true;
break;
}
}
if(setBonds){
IAtomContainer ret = possibleCopy;
if(possibleCopy ==container && makeCopy){
try {
ret = safeClone(container);
} catch (Exception e) {
//shouldn't happen container support clones
}
}
Kekulization.kekulize(ret);
for(IBond bond : ret.bonds()){
bond.setIsAromatic(false);
}
return ret;
}
for(IBond bond : possibleCopy.bonds()){
bond.setIsAromatic(false);
}
return possibleCopy;
}
public static IAtomContainer setImplicitHydrogensIfNeeded(IAtomContainer container, boolean makeCopy) throws CDKException {
boolean recompute=false;
for(IAtom atom : container.atoms()){
if(atom.getImplicitHydrogenCount() ==null){
recompute=true;
break;
}
}
if(!recompute){
return container;
}
IAtomContainer ret = container;
if(makeCopy){
try {
ret = container.clone();
} catch (CloneNotSupportedException e) {
//shouldn't happen container support clones
}
}
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ret);
CDKHydrogenAdder.getInstance(ret.getBuilder()).addImplicitHydrogens(ret);
return ret;
}
public static IAtomContainer toAtomContainer(Chemical chemical){
return (IAtomContainer) chemical.getImpl().getWrappedObject();
}
public static IChemObjectBuilder getChemObjectBuilder() {
return SilentChemObjectBuilder.getInstance();
}
public static IAtomContainer parseSmarts(String smarts) throws CDKException, IOException {
IAtomContainer container =CdkUtil.getChemObjectBuilder().newAtomContainer();
Smarts.parse(container, smarts);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
QueryAtomPerceptor.percieve(container);
return container;
}
public static void removeQueryAtoms(IAtomContainer containerToFingerprint) {
//iterator.remove() doesn't seem to work
List indexesToRemove = new ArrayList<>();
int i=0;
for(IAtom next : containerToFingerprint.atoms()){
if(next.getSymbol() ==null){
indexesToRemove.add(Integer.valueOf(i));
}
i++;
}
final IAtomContainer fia=containerToFingerprint;
//iterate in reverse to not mess up atom order of deletions
Comparator ci=Comparator.naturalOrder();
indexesToRemove.stream().sorted(ci.reversed()).forEach(k->{
fia.removeAtom(k);
});
}
public static void removeQueryBonds(IAtomContainer containerToFingerprint) {
Iterator bondIter = containerToFingerprint.bonds().iterator();
while(bondIter.hasNext()){
IBond next = bondIter.next();
if(next.getOrder() ==null || next.getOrder() == Order.UNSET){
if(!next.isAromatic()) {
if(CdkUtil.isSubtleQueryBond(next)
&& !CdkUtil.simplifyQBond(next)
) {
bondIter.remove();
}
}
}
}
}
public static IAtomContainer getSimplifiedContainer(IAtomContainer iac) {
if(iac instanceof QueryAtomContainer) {
QueryAtomContainer qac = (QueryAtomContainer)iac;
CdkChemicalImpl cci = new CdkChemicalImpl(qac, (ChemicalSource)null);
Chemical cq = new Chemical(cci);
Chemical qq=cq.copy();
IAtomContainer ii = (IAtomContainer)qq.getImpl().getWrappedObject();
return ii;
}
return iac;
}
private static String getSymbolForAtomExpression(Expr exp){
List elist = new ArrayList<>();
getLeafNodes(exp, elist);
if(elist.size()>0 && elist.stream()
.allMatch(ex->ex.type().equals(Expr.Type.ELEMENT))){
return "L";
}else{
return "A";
}
}
public static void getLeafNodes(Expr exr, List elist){
if(exr.type().equals(Expr.Type.OR) || exr.type().equals(Expr.Type.AND)){
getLeafNodes(exr.left(), elist);
getLeafNodes(exr.right(), elist);
}else if(exr.type().equals(Expr.Type.NOT)){
getLeafNodes(exr.left(), elist);
}else{
elist.add(exr);
}
}
public static void navNodes(Expr exr, BiConsumer elist, int l){
elist.accept(l, exr);
if(exr.type().equals(Expr.Type.OR) || exr.type().equals(Expr.Type.AND)){
navNodes(exr.left(), elist,l+1);
navNodes(exr.right(), elist,l+1);
}else if(exr.type().equals(Expr.Type.NOT)){
navNodes(exr.left(), elist,l+1);
}
}
public static String rep(String m, int l){
String r="";
for(int i=0;i © 2015 - 2025 Weber Informatics LLC | Privacy Policy