/*
Copyright Ideaconsult Ltd. (C) 2005-2007
Contact: nina@acad.bg
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This program is distributed in the hope that it will be useful,
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*//**
* Created on 2005-5-2
* @author Nina Jeliazkova nina@acad.bg
*
* Project : toxtree
* Package : toxTree.tree.rules
* Filename: RuleSomeBenzeneDerivatives.java
*/
package toxTree.tree.cramer;
import java.util.ArrayList;
import java.util.List;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import toxTree.exceptions.DecisionMethodException;
import toxTree.query.FunctionalGroups;
import toxTree.query.MolAnalyser;
import toxTree.query.MolFlags;
import toxTree.tree.rules.RuleRingAllowedSubstituents;
/**
* Rule 6 of the Cramer scheme (see {@link toxTree.tree.cramer.CramerRules})
* @author Nina Jeliazkova
* @version 0.1, 2005-5-2
*/
public class RuleSomeBenzeneDerivatives extends RuleRingAllowedSubstituents {
public static final transient String MSG_ALKOXYPARACH="Alkoxy group para to hydrocarbon chain susbtituent\t";
public static final transient String MSG_BENZENESUBSTITUENT = "Benzene substituent found:\t";
protected int index_hydroxy1 = 0;
//protected int index_hydroxyEsterSubstituted = 1;
protected int index_hydroxy = 1;
protected int index_ester = 2;
protected int index_alkoxy = 3;
protected int index_hydrocarbon = 4;
protected ArrayList chIDs, hydroxyIDs, alkoxyIDs;
protected int[] places = {-1,-1,-1,-1,-1,-1};
protected QueryAtomContainer ring6 = null;
/**
* Comment for serialVersionUID
*/
private static final long serialVersionUID = 7287247707766324579L;
/**
* Constructor
*
*/
public RuleSomeBenzeneDerivatives() {
super();
setAnalyzeAromatic(true);
setAnalyzeOnlyRingsWithFlagSet(true);
chIDs = new ArrayList();
chIDs.add(FunctionalGroups.CH);chIDs.add(FunctionalGroups.CH2);chIDs.add(FunctionalGroups.CH3);
hydroxyIDs = new ArrayList();
hydroxyIDs.add(FunctionalGroups.HYDROXY1);
//hydroxyIDs.add(FunctionalGroups.HYDROXYESTERSUBSTITED);
hydroxyIDs.add(FunctionalGroups.ALCOHOL);
hydroxyIDs.add(FunctionalGroups.ESTER);
hydroxyIDs.add(FunctionalGroups.CH);
hydroxyIDs.add(FunctionalGroups.CH2);
hydroxyIDs.add(FunctionalGroups.CH3);
alkoxyIDs = new ArrayList();alkoxyIDs.add(FunctionalGroups.ETHER);
alkoxyIDs.add(FunctionalGroups.CH);alkoxyIDs.add(FunctionalGroups.CH2);alkoxyIDs.add(FunctionalGroups.CH3);
ring6 = FunctionalGroups.ring(6);
addSubstructure(FunctionalGroups.hydroxy1());
//addSubstructure(FunctionalGroups.hydroxyEsterSubstituted());
addSubstructure(FunctionalGroups.alcohol(false));
addSubstructure(FunctionalGroups.ester());
addSubstructure(FunctionalGroups.alkoxy()); //alkoxy
id = "6";
title = "Benzene derivative with certain substituents";
explanation.append("Is the substance a benzene derivative bearing substituents consisting only of ");
explanation.append("- (a)hydrocarbon chains or 1'hydroxy or hydroxy ester-substituted hydrocarbon chains and");
explanation.append("
- (b)one or more alkoxy groups, one of which must be para to the hydrocarbon chain in (a)?");
explanation.append("
this places in class III safrole, myristicin and related substances.");
examples[0] = "COC1=CC(CC=C)=CC=C1O";
examples[1] = "C=CCC1=CC=C2OCOC2=C1";
editable = false;
}
@Override
protected IRingSet hasRingsToProcess(IAtomContainer mol) throws DecisionMethodException {
MolFlags mf = (MolFlags) mol.getProperty(MolFlags.MOLFLAGS);
if (mf == null) throw new DecisionMethodException(ERR_STRUCTURENOTPREPROCESSED);
IRingSet rings = mf.getRingset();
if (rings == null) {
logger.fine("Acyclic structure");
return null;
}
int benzene = 0;
for (int i=0; i < rings.getAtomContainerCount(); i++) {
IRing r = (IRing) rings.getAtomContainer(i);
if (r.getAtomCount() != 6 ) continue;
if (!r.getFlag(CDKConstants.ISAROMATIC)) continue;
Object o = r.getProperty(MolAnalyser.HETEROCYCLIC);
if ((o!=null) && ((Boolean) o).booleanValue()) continue;
benzene ++;
}
if (benzene == 1) {
logger.fine("Benzene ring found.");
return rings;
} else {
if (benzene > 1) logger.fine("Too many benzene rings found.");
else logger.fine("No benzene rings found.");
return null;
}
}
/* (non-Javadoc)
* @see toxTree.tree.rules.RuleRingAllowedSubstituents#substituentIsAllowed(org.openscience.cdk.AtomContainer)
*/
@Override
public boolean substituentIsAllowed(IAtomContainer a, int[] place)
throws DecisionMethodException {
//(a)hydrocarbon chain
//FunctionalGroups.markCHn(a);
//logger.fine(FunctionalGroups.mapToString(a));
if (FunctionalGroups.hasMarkedOnlyTheseGroups(a,chIDs)) {
for (int j=0;j=0) places[place[j]] = index_hydrocarbon;
logger.fine(MSG_BENZENESUBSTITUENT+"hydrocarbon chain\tat place\t"+place);
return true;
}
QueryAtomContainer q = (QueryAtomContainer)getSubstructure(index_hydroxy1);
List list = FunctionalGroups.getBondMap(a,q,true);
if (list != null) {
//FunctionalGroups.markMaps(a,q,list);
if (FunctionalGroups.hasMarkedOnlyTheseGroups(a,hydroxyIDs)) {
for (int j=0;j=0) places[place[j]] = index_hydroxy1;
logger.fine(MSG_BENZENESUBSTITUENT+"1'-hydroxy hydrocarbon chain");
return true;
}
}//clear hydroxy mark ?
/*
q = (QueryAtomContainer)getSubstructure(index_hydroxyEsterSubstituted);
list = FunctionalGroups.getBondMap(a,q,true);
if (list != null) {
//FunctionalGroups.markMaps(a,q,list);
if (FunctionalGroups.hasMarkedOnlyTheseGroups(a,hydroxyIDs)) {
for (int j=0;j=0) places[place[j]] = index_hydroxyEsterSubstituted;
logger.fine(MSG_BENZENESUBSTITUENT,"hydroxy ester substituted hydrocarbon chain");
return true;
}
}
*/
q = (QueryAtomContainer)getSubstructure(index_hydroxy);
list = FunctionalGroups.getUniqueBondMap(a,q,true);
if (list != null) FunctionalGroups.markMaps(a,q,list);
q = (QueryAtomContainer)getSubstructure(index_ester);
list = FunctionalGroups.getUniqueBondMap(a,q,true);
if (list != null) FunctionalGroups.markMaps(a,q,list);
if (FunctionalGroups.hasMarkedOnlyTheseGroups(a,hydroxyIDs)) {
for (int j=0;j=0) places[place[j]] = index_ester;
logger.fine(MSG_BENZENESUBSTITUENT+"hydroxy ester substituted hydrocarbon chain");
return true;
}
q = (QueryAtomContainer)getSubstructure(index_alkoxy);
list = FunctionalGroups.getBondMap(a,q,true);
if (list != null) {
//FunctionalGroups.markMaps(a,q,list);
if (FunctionalGroups.hasMarkedOnlyTheseGroups(a,alkoxyIDs)) {
for (int j=0;j=0) places[place[j]] = index_alkoxy;
logger.fine(MSG_BENZENESUBSTITUENT+"alkoxy group at place\t"+place);
return true;
}
}
logger.fine("Forbiden benzene substituent found");
return false;
}
/* (non-Javadoc)
* @see toxTree.tree.rules.RuleSubstructures#isImplemented()
*/
@Override
public boolean isImplemented() {
return true;
}
@Override
public boolean verifyRule(IAtomContainer mol) throws DecisionMethodException {
logger.finer(toString());
IRingSet rs = hasRingsToProcess(mol);
if (rs == null) return false;
for (int i=0;i<6;i++) places[i] = -1;
FunctionalGroups.markCHn(mol);
//if entire structure has only allowed groups, return true (can't have other groups as substituents)
FunctionalGroups.hasOnlyTheseGroups(mol,query,ids,false);
// logger.fine(FunctionalGroups.mapToString(mol));
//otherwise some of the forbidden groups can be in-ring, so substituents can be fine
//iterating over all rings in the ringset
IRing r =null;
for (int i=0; i < rs.getAtomContainerCount(); i++) {
r = (IRing) rs.getAtomContainer(i);
if (!analyze(r)) continue;
logger.fine("Ring\t"+(i+1));
//new atomcontainer with ring atoms/bonds deleted
IAtomContainer mc = FunctionalGroups.cloneDiscardRingAtomAndBonds(mol,r);
logger.fine("\tmol atoms\t"+mc.getAtomCount());
FunctionalGroups.markAtomsInRing(mol,ring6);
IMoleculeSet s = ConnectivityChecker.partitionIntoMolecules(mc);
//logger.fine("Ring substituents\t",s.getMoleculeCount());
int substituents = 0;
for (int k = 0; k < s.getMoleculeCount(); k++) {
IMolecule m = s.getMolecule(k);
if (m!=null) {
if ((m.getAtomCount() == 1) && (m.getAtom(0).getSymbol().equals("H"))) continue;
Object place = null;
int[] p = new int[m.getAtomCount()];
for (int j=0;j