RubyGems - toxtree - Versions diffs - 0.0.1 - Mend

toxtree 0.0.1

Files changed (1384) hide show

data/Toxtree-v2.6.13/src/verhaar/categories/Class5Unknown.java ADDED

@@ -0,0 +1,66 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2013
+Contact: www.ideaconsult.net
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+This program 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 General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package verhaar.categories;
+import toxTree.tree.DefaultCategory;
+/**
+ *
+ * Class 5 Not possible to classify according to these rules.
+ * @author Nina Jeliazkova nina@acad.bg
+ * <b>Modified</b> Dec 17, 2006
+ */
+public class Class5Unknown extends DefaultCategory {
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = 2349050959864652279L;
+	/**
+	 *
+	 */
+	public Class5Unknown() {
+		super("Class 5 (Not possible to classify according to these rules)",5);
+		setExplanation("<html><h3>Unknown</h3>Compounds that cannot be classified as belonging to class 1, 2 or 3 <br>and that are not known to be compounds acting by a specific mechanism can only be classified as \"not possible to classify according to these rules\".<html>");
+		setThreshold("");
+	}
+	/**
+	 * @param name
+	 * @param id
+	 */
+	public Class5Unknown(String name, int id) {
+		super(name, id);
+	}
+		@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.InconclusiveCategory;
+	}
+}

data/Toxtree-v2.6.13/src/verhaar/categories/package.html ADDED

@@ -0,0 +1,16 @@
+<HTML><HEAD><TITLE>Toxtreee plugin</TITLE>
+<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
+</SCRIPT>
+<META NAME="Description" CONTENT="toxTree application">
+<META NAME="Keywords" CONTENT="source,decision tree,TTC,java">
+<!--  -->
+<body bgColor="#FFFFFF" link="#428EFF">
+The package contains implementations of {@link toxTree.core.IDecisionCategory} categories for
+{@link verhaar.VerhaarScheme} decision tree.
+</body></HTML>

data/Toxtree-v2.6.13/src/verhaar/package.html ADDED

@@ -0,0 +1,20 @@
+<HTML><HEAD><TITLE>Toxtree plugin</TITLE>
+<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
+</SCRIPT>
+<META NAME="Description" CONTENT="toxTree application">
+<META NAME="Keywords" CONTENT="source,decision tree,TTC,java">
+<!--  -->
+<body bgColor="#FFFFFF" link="#428EFF">
+Class {@link verhaar.VerhaarScheme} is the implementation of Verhaar structural scheme for estimating toxicity mode of action.
+<hr>
+<ul>
+<li>Verhaar HJM, van Leeuwen CJ and Hermens JLM (1992) Classifying environmental pollutants. 1. Structure-activity relationships for prediction of aquatic toxicity. Chemosphere 25, 471-491.
+<li>Verhaar HJM, Mulder W and Hermens JLM (1995) QSARs for ecotoxicity. In: Overview of structure-activity relationships for environmental endpoints, Part 1: General outline and procedure. Hermens JLM (Ed), Report prepared within the framework of the project "QSAR for Prediction of Fate and Effects of Chemicals in the Environment", an international project of the Environment; Technologies RTD Programme (DGXII/D-1) of the Europenan Commission under contract number EV5V-CT92-0211.
+<li>Verhaar HJM, Solbe J, Speksnijder J, van Leeuwen CJ and Hermens JLM (2000) Classifying environmental pollutants: Part 3. External validation of the classification system. Chemosphere 40, 875-883.
+</ul>
+</body></HTML>

data/Toxtree-v2.6.13/src/verhaar/query/AromaticQueryBond.java ADDED

@@ -0,0 +1,63 @@
+/*
+Copyright Nina Jeliazkova (C) 2005-2006
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+This program 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 General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package verhaar.query;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.isomorphism.matchers.IQueryAtom;
+/**
+ * A fix until {@link AromaticQueryBond} is fixed
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-10-30
+ */
+public class AromaticQueryBond extends
+		org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond {
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = 7143741142261301599L;
+	/**
+	 *
+	 */
+	public AromaticQueryBond() {
+		super();
+		// TODO Auto-generated constructor stub
+	}
+	/**
+	 * @param atom1
+	 * @param atom2
+	 * @param order
+	 */
+	public AromaticQueryBond(IQueryAtom atom1, IQueryAtom atom2) {
+		super(atom1, atom2, IBond.Order.SINGLE); //TODO bond order doesn't matter
+		// TODO Auto-generated constructor stub
+	}
+	public boolean matches(IBond bond) {
+        if (bond.getFlag(CDKConstants.ISAROMATIC)) {
+            return true;
+        }
+        return false;
+    };
+}

data/Toxtree-v2.6.13/src/verhaar/query/FunctionalGroups.java ADDED

@@ -0,0 +1,429 @@
+/*
+Copyright Nina Jeliazkova (C) 2005-2006
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+This program 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 General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package verhaar.query;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.isomorphism.matchers.IQueryAtom;
+import org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom;
+import org.openscience.cdk.isomorphism.matchers.OrderQueryBond;
+import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
+import org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom;
+import org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom;
+import org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom;
+import org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom;
+import org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import toxTree.query.ReallyAnyAtom;
+import toxTree.query.TopologyAnyBond;
+import toxTree.query.TopologyOrderQueryBond;
+import ambit2.core.data.MoleculeTools;
+/**
+ * A singleton class providing static methods for various functional groups in {@link verhaar.VerhaarScheme}.
+ * In future could be modified to use a different approach rather than static methods.
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-10-30
+ */
+public class FunctionalGroups extends toxTree.query.FunctionalGroups {
+	public static final String IONICGROUP = "IONICGROUP";
+	public static final String RINGSUBSTITUTED = "RINGSUBSTITUTED";
+	public static final String HALOGEN_BETA_FROM_UNSATURATION = "HALOGEN_BETA_FROM_UNSATURATION";
+	public static final String HALOGEN_ALPHA_FROM_UNSATURATION = "HALOGEN_ALPHA_FROM_UNSATURATION";
+	public static final String HALOGEN = "HALOGEN";
+	public static final String EPOXIDE = "EPOXIDE";
+	public static final String AZARIDINE = "AZARIDINE";
+	public static final String PEROXIDE = "PEROXIDE";
+	public static final String PHENOL = "PHENOL";
+	public static final String ANILINE = "ANILINE";
+	public static final String PYRIDINE = "PYRIDINE";
+	public static final String BENZYLALCOHOL = "BENZYLALCOHOL";
+	public static final String KETONE_A_B_UNSATURATED = "KETONE_A_B_UNSATURATED";
+	public static final String CYCLICESTER = "CYCLICESTER";
+    public static final String n = "n";
+	/**
+	 *
+	 */
+	protected FunctionalGroups() {
+		super();
+	}
+	public static QueryAtomContainer ionicGroup() {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(IONICGROUP);
+		AnyAtom a1 = new ReallyAnyAtom();
+		AnyAtom a2 = new ReallyAnyAtom();
+		q.addAtom(a1);q.addAtom(a2);
+		q.addBond(new QueryAssociationBond(a1,a2));
+		return q;
+	}
+	public static QueryAtomContainer ringSubstituted(String substituent) {
+		QueryAtomContainer q = new QueryAtomContainer();
+		if (substituent == null)
+			q.setID(RINGSUBSTITUTED);
+		else q.setID(RINGSUBSTITUTED+substituent);
+		IAtom a[] = new IAtom[3];
+		for (int i=0;i<a.length;i++) {
+			if (i==1) {
+				a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+			} else a[i] = new ReallyAnyAtom();
+			q.addAtom(a[i]);
+			if (i > 0) {
+				TopologyAnyBond b = new TopologyAnyBond(a[i],a[i-1],true);
+				q.addBond(b);
+			}
+		}
+		if (substituent != null) {
+				SymbolQueryAtom s = new SymbolQueryAtom(
+						new org.openscience.cdk.Atom(substituent));
+				q.addAtom(s);
+				q.addBond(new TopologyAnyBond(a[1],s,false));
+			}
+		return q;
+	}
+	/**
+	 * Halogen at alpha position from unsaturation.
+	 * "X=X[Hal]"
+	 * @return
+	 */
+	public static QueryAtomContainer halogenAtAlphaFromUnsaturation(String[] halogens) {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(HALOGEN_ALPHA_FROM_UNSATURATION);
+		IAtom a[] = new IAtom[3];
+		for (int i=0;i<a.length;i++) {
+			if (i==2) {
+				a[i] = new SymbolSetQueryAtom();
+				for (int j=0; j < halogens.length;j++)
+					((SymbolSetQueryAtom)a[i]).addSymbol(halogens[j]);
+			} else a[i] = new ReallyAnyAtom();
+			q.addAtom(a[i]);
+			switch (i) {
+			case 0: break;
+			case 1: {
+				q.addBond(new QueryUnsaturatedBond(a[i],a[i-1]));
+				break;
+			}
+			default: {
+				q.addBond(new OrderQueryBondAromatic((IQueryAtom)a[i],(IQueryAtom)a[i-1],CDKConstants.BONDORDER_SINGLE,false));
+				break;
+			}
+			}
+		}
+		return q;
+	}
+	/**
+	 * Halogen at beta position from unsaturation.
+	 * "X=XX[Hal]"
+	 * @return
+	 */
+	public static QueryAtomContainer halogenAtBetaFromUnsaturation(String[] halogens) {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(HALOGEN_BETA_FROM_UNSATURATION);
+		IAtom a[] = new IAtom[4];
+		for (int i=0;i<a.length;i++) {
+			if (i==3) {
+				a[i] = new SymbolSetQueryAtom();
+				for (int j=0; j < halogens.length;j++)
+					((SymbolSetQueryAtom)a[i]).addSymbol(halogens[j]);
+			} else a[i] = new ReallyAnyAtom();
+			q.addAtom(a[i]);
+			switch (i) {
+			case 0: break;
+			case 1: {
+				q.addBond(new QueryUnsaturatedBond(a[i],a[i-1]));
+				break;
+			}
+			default: {
+				q.addBond(new OrderQueryBondAromatic((IQueryAtom)a[i],(IQueryAtom)a[i-1],CDKConstants.BONDORDER_SINGLE,false));
+				break;
+			}
+			}
+		}
+		return q;
+	}
+	public static QueryAtomContainer halogen() {
+		String[] h = {"Cl","F","Br","I"};
+		return halogen(h);
+	}
+	public static QueryAtomContainer halogen(String[] halogens) {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(HALOGEN);
+		SymbolSetQueryAtom h = new SymbolSetQueryAtom();
+		h.setSymbol("*");
+		for (int j=0; j < halogens.length;j++)
+			h.addSymbol(halogens[j]);
+		InverseSymbolSetQueryAtom a = new InverseSymbolSetQueryAtom();
+		a.setSymbol("*");  //so the bond could be marked
+		//a.setProperty(DONTMARK,q.getID());
+		q.addAtom(h);
+		q.addAtom(a);
+		q.addBond(new AnyOrderQueryBond((IQueryAtom)a,(IQueryAtom)h,CDKConstants.BONDORDER_SINGLE));
+		return q;
+	}
+	public static QueryAtomContainer epoxide() {
+		QueryAtomContainer q = createQuery("C1OC1",EPOXIDE);
+		return q;
+	}
+	public static QueryAtomContainer azaridine() {
+		QueryAtomContainer q = createQuery("C1NC1",AZARIDINE);
+		return q;
+	}
+	public static QueryAtomContainer peroxide() {
+		QueryAtomContainer q = createQuery("OO",PEROXIDE);
+		return q;
+	}
+	public static QueryAtomContainer phenol() {
+		IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(PHENOL);
+		IAtom[] a = new IAtom[6];
+		for (int i=0;i<a.length;i++) {
+			a[i] = new SymbolQueryAtom(MoleculeTools.newAtom(builder,"C"));
+			q.addAtom(a[i]);
+			if (i > 0) {
+				q.addBond(new  verhaar.query.AromaticQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1]));
+			}
+		}
+		q.addBond(new verhaar.query.AromaticQueryBond((IQueryAtom)a[0],(IQueryAtom)a[5]));
+		SymbolQueryAtom o = new SymbolQueryAtom(MoleculeTools.newAtom(builder,"O"));
+		q.addAtom(o);
+		SymbolQueryAtom h = new SymbolQueryAtom(MoleculeTools.newAtom(builder,"H"));
+		q.addAtom(h);
+		q.addBond(new OrderQueryBond(o,h,CDKConstants.BONDORDER_SINGLE));
+		q.addBond(new OrderQueryBond(o,(IQueryAtom)a[0],CDKConstants.BONDORDER_SINGLE));
+		return q;
+	}
+	public static QueryAtomContainer aniline() {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(ANILINE);
+		IAtom[] a = new IAtom[6];
+		for (int i=0;i<a.length;i++) {
+			a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+			q.addAtom(a[i]);
+			if (i > 0) {
+				q.addBond(new  verhaar.query.AromaticQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1]));
+			}
+		}
+		q.addBond(new verhaar.query.AromaticQueryBond((IQueryAtom)a[0],(IQueryAtom)a[5]));
+		SymbolQueryAtom o = new SymbolQueryAtom(new org.openscience.cdk.Atom("N"));
+		q.addAtom(o);
+		SymbolQueryAtom h = new SymbolQueryAtom(new org.openscience.cdk.Atom("H"));
+		q.addAtom(h);
+		q.addBond(new OrderQueryBond(o,h,CDKConstants.BONDORDER_SINGLE));
+		q.addBond(new OrderQueryBond(o,(IQueryAtom)a[0],CDKConstants.BONDORDER_SINGLE));
+		return q;
+	}
+	public static QueryAtomContainer pyridine() {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(PYRIDINE);
+		IAtom[] a = new IAtom[6];
+		for (int i=0;i<a.length;i++) {
+			if (i==0) a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("N"));
+			else a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+			q.addAtom(a[i]);
+			if (i > 0) {
+				q.addBond(new  verhaar.query.AromaticQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1]));
+			}
+		}
+		q.addBond(new verhaar.query.AromaticQueryBond((IQueryAtom)a[0],(IQueryAtom)a[5]));
+		return q;
+	}
+	public static QueryAtomContainer pyridine_character() {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(PYRIDINE);
+		IAtom[] a = new IAtom[6];
+		for (int i=0;i<a.length;i++) {
+			if (i==0) a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("N"));
+			else {
+				SymbolSetQueryAtom set = new SymbolSetQueryAtom();
+				set.addSymbol("C");
+				set.addSymbol("N");
+				a[i] = set;
+			}
+			q.addAtom(a[i]);
+			if (i > 0) {
+				q.addBond(new  verhaar.query.AromaticQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1]));
+			}
+		}
+		q.addBond(new verhaar.query.AromaticQueryBond((IQueryAtom)a[0],(IQueryAtom)a[5]));
+		return q;
+	}
+	public static QueryAtomContainer benzylAlcohol() {
+		QueryAtomContainer q = createQuery("c1ccccc1CO[H]",BENZYLALCOHOL);
+		try {
+			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(q);
+			CDKHueckelAromaticityDetector.detectAromaticity(q);
+		} catch (CDKException x) {
+			//FunctionalGroups.logger.error(x);
+			x.printStackTrace();
+		}
+		return q;
+	}
+	public static QueryAtomContainer ketone_a_b_unsaturated() {
+		QueryAtomContainer q = new QueryAtomContainer();
+		q.setID(KETONE_A_B_UNSATURATED);
+		IAtom[] a = new IAtom[5];
+		for (int i=0; i < a.length; i++) {
+			switch (i) {
+			case 0: { a[i] = new ReallyAnyAtom(); break;}
+			case 1: { a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+					q.addBond(new QueryUnsaturatedBond(a[0],a[1]));
+					break;}
+			case 2: {
+				a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+				q.addBond(new OrderQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1],CDKConstants.BONDORDER_SINGLE));
+				break;}
+			case 3: { a[i] = new SymbolQueryAtom(new org.openscience.cdk.Atom("O"));
+					q.addBond(new OrderQueryBond((IQueryAtom)a[i],(IQueryAtom)a[i-1],CDKConstants.BONDORDER_DOUBLE));
+					break;}
+			case 4: {
+				a[i] = new SymbolSetQueryAtom();
+				((SymbolSetQueryAtom)a[i]).addSymbol("C");
+				((SymbolSetQueryAtom)a[i]).addSymbol("H");
+				q.addBond(new OrderQueryBond((IQueryAtom)a[i],(IQueryAtom)a[2],CDKConstants.BONDORDER_SINGLE));
+				break;}
+			}
+			q.addAtom(a[i]);
+		}
+		return q;
+	}
+	public static IMolecule makeNitroPhenol() {
+		 IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+		  IMolecule mol = MoleculeTools.newMolecule(SilentChemObjectBuilder.getInstance());
+		  IAtom a1 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a1);
+		  IAtom a2 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a2);
+		  IAtom a3 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a3);
+		  IAtom a4 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a4);
+		  IAtom a5 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a5);
+		  IAtom a6 = MoleculeTools.newAtom(builder,"C");
+		  mol.addAtom(a6);
+		  IAtom a7 = MoleculeTools.newAtom(builder,"O");
+		  mol.addAtom(a7);
+		  IAtom a8 = MoleculeTools.newAtom(builder,"N");
+		  mol.addAtom(a8);
+		  IAtom a9 = MoleculeTools.newAtom(builder,"O");
+		  mol.addAtom(a9);
+		  IAtom a10 = MoleculeTools.newAtom(builder,"O");
+		  mol.addAtom(a10);
+		  IBond b1 = MoleculeTools.newBond(builder, a1, a2, IBond.Order.DOUBLE);
+		  mol.addBond(b1);
+		  IBond b2 = MoleculeTools.newBond(builder,a2, a3, IBond.Order.SINGLE);
+		  mol.addBond(b2);
+		  IBond b3 = MoleculeTools.newBond(builder,a3, a4, IBond.Order.DOUBLE);
+		  mol.addBond(b3);
+		  IBond b4 = MoleculeTools.newBond(builder,a4, a5, IBond.Order.SINGLE);
+		  mol.addBond(b4);
+		  IBond b5 = MoleculeTools.newBond(builder,a5, a6, IBond.Order.DOUBLE);
+		  mol.addBond(b5);
+		  IBond b6 = MoleculeTools.newBond(builder,a6, a1, IBond.Order.SINGLE);
+		  mol.addBond(b6);
+		  IBond b7 = MoleculeTools.newBond(builder,a4, a7, IBond.Order.SINGLE);
+		  mol.addBond(b7);
+		  IBond b8 = MoleculeTools.newBond(builder,a2, a8, IBond.Order.SINGLE);
+		  mol.addBond(b8);
+		  IBond b9 = MoleculeTools.newBond(builder,a8, a9, IBond.Order.DOUBLE);
+		  mol.addBond(b9);
+		  IBond b10 = MoleculeTools.newBond(builder,a8, a10, IBond.Order.DOUBLE);
+		  mol.addBond(b10);
+		  return mol;
+		}
+	public static QueryAtomContainer createAutoQueryContainer(String smiles) {
+		return createAutoQueryContainer(createAtomContainer(smiles,false,smiles));
+	}
+    public static QueryAtomContainer createAutoQueryContainer(IAtomContainer container) {
+        QueryAtomContainer queryContainer = new QueryAtomContainer();
+        for (int i = 0; i < container.getAtomCount(); i++) {
+        	IAtom atom = container.getAtom(i);
+        	if (atom instanceof IPseudoAtom)
+        		queryContainer.addAtom(new ReallyAnyAtom());
+        	else if (atom.getSymbol().equals("X")) { //halogen
+        		SymbolSetQueryAtom a = new SymbolSetQueryAtom();
+        		a.addSymbol("Cl");
+        		a.addSymbol("Br");
+        		a.addSymbol("F");
+        		a.addSymbol("I");
+        	} else queryContainer.addAtom(new SymbolAndChargeQueryAtom(atom));
+        }
+        for (int i = 0; i < container.getBondCount(); i++) {
+        	IBond bond = container.getBond(i);
+            int index1 = container.getAtomNumber(bond.getAtom(0));
+            int index2 = container.getAtomNumber(bond.getAtom(1));
+            if (bond.getFlag(CDKConstants.ISAROMATIC)) {
+                queryContainer.addBond(new verhaar.query.AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1),
+                                      (IQueryAtom) queryContainer.getAtom(index2)));
+            } else {
+                queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1),
+                                      (IQueryAtom) queryContainer.getAtom(index2),
+                                      bond.getOrder()));
+            }
+        }
+        return queryContainer;
+    }
+    //TODO cyclic sulphonic/sulphuric esters
+    public static QueryAtomContainer cyclicEster() {
+        QueryAtomContainer query = new QueryAtomContainer();
+        query.setID(CYCLICESTER);
+        AnyAtom r = new ReallyAnyAtom();
+        r.setProperty(DONTMARK,query.getID());
+        InverseSymbolSetQueryAtom e = new InverseSymbolSetQueryAtom();
+        e.addSymbol("H");
+        e.setProperty(DONTMARK,query.getID());
+        SymbolQueryAtom c = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
+        SymbolQueryAtom o1 = new SymbolQueryAtom(new org.openscience.cdk.Atom("O"));
+        SymbolQueryAtom o2 = new SymbolQueryAtom(new org.openscience.cdk.Atom("O"));
+        query.addAtom(r); query.addAtom(e); query.addAtom(c);
+        query.addAtom(o1); query.addAtom(o2);
+        query.addBond(new OrderQueryBond(r, c, CDKConstants.BONDORDER_SINGLE));
+        query.addBond(new TopologyOrderQueryBond(c, o1, CDKConstants.BONDORDER_SINGLE,true));
+        query.addBond(new OrderQueryBond(c, o2, CDKConstants.BONDORDER_DOUBLE));
+        query.addBond(new OrderQueryBond(o1, e, CDKConstants.BONDORDER_SINGLE));
+        return query;
+    }
+}