toxtree 0.0.1

data/Toxtree-v2.6.13/src/mutant/rules/SA9_gen.java

@@ -0,0 +1,54 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007  
+
+Contact: nina@acad.bg
+
+This program 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.
+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 Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package mutant.rules;
+
+import java.util.logging.Level;
+
+import toxTree.tree.rules.StructureAlert;
+import ambit2.smarts.query.SMARTSException;
+
+public class SA9_gen extends StructureAlert {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 5739165398205328879L;
+
+	public SA9_gen() {
+		try {
+			super.initSingleSMARTS(super.smartsPatterns,"alkyl nitrite", "O=[NX2]OC");
+			setID("SA9_gen");
+			setTitle("Alkyl nitrite");
+			setExplanation("");
+			
+			examples[0] = "O=NC";
+			examples[1] = "CC(C)CON=O";	
+			editable = false;
+		} catch (SMARTSException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+		}	
+	}
+
+}

data/Toxtree-v2.6.13/src/mutant/rules/SMARTSGroup.java

@@ -0,0 +1,60 @@
+/* SMARTSGroup.java
+ * Author: Nina Jeliazkova
+ * Date: Jan 6, 2008 
+ * Revision: 0.1 
+ * 
+ * Copyright (C) 2005-2006  Nina Jeliazkova
+ * 
+ * Contact: nina@acad.bg
+ * 
+ * This program 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.
+ * 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * 
+ */
+
+package mutant.rules;
+
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+
+public class SMARTSGroup {
+    
+    protected String name;
+    protected String smarts;
+    protected IAtomContainerSet[] examples;
+    
+    public synchronized IAtomContainerSet getExamples(boolean value) {
+        if (value) return examples[1];
+        else return examples[0];
+    }
+    public synchronized void setExamples(boolean result,IAtomContainerSet examples) {
+        if (result) this.examples[1] = examples;
+        else this.examples[0] = examples;
+    }
+    public synchronized String getName() {
+        return name;
+    }
+    public synchronized void setName(String name) {
+        this.name = name;
+    }
+    public synchronized String getSmarts() {
+        return smarts;
+    }
+    public synchronized void setSmarts(String smarts) {
+        this.smarts = smarts;
+    }
+}

data/Toxtree-v2.6.13/src/mutant/rules/SMARTSgroups.java

@@ -0,0 +1,56 @@
+/* SMARTSgroups.java
+ * Author: Nina Jeliazkova
+ * Date: Jan 6, 2008 
+ * Revision: 0.1 
+ * 
+ * Copyright (C) 2005-2006  Nina Jeliazkova
+ * 
+ * Contact: nina@acad.bg
+ * 
+ * This program 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.
+ * 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * 
+ */
+
+package mutant.rules;
+
+
+public class SMARTSgroups {
+    public static String NITRO_CHARGED = "[N+](=O)[O-]";
+    public static String NITRO_UNCHARGED = "N(=O)(=O)";
+    public static String AROMATIC_AMINE = "[NX3H2]";
+    
+/*
+    {"Nitro aromatic","c[N+](=O)[O-]","O=[N+]([O-])C=1C=CC=C(C=1)Cl","NA27",new Boolean(false)},
+    {"Primary aromatic amine","c[N]([#1,C])([#1,C])","CNC=1C([H])=C([H])C([H])=C(Cl)C=1([H])","NA28",new Boolean(false)},
+    {"Hydroxyl amine","cN([OX2H])([#1,C])","[H]ONC1=CC=CC=C1Cl","NA28",new Boolean(false)},
+    {"Hydroxyl amine ester","cN([#1,C])OC=O","CCCN(OC=O)C1=CC=CC=C1(Cl)","NA28",new Boolean(false)},
+    {"Aromatic mono- and dialkylamine","c[NX3v3]([#1,CH3])([#1,CH3])","CNC=1C=CC=C(Cl)C=1","NA28bis",new Boolean(false)},        
+    {"Aromatic mono- and dialkylamine","c[NX3v3]([#1,CH3])([CH2][CH3])","CCN(C)C=1C=CC=C(C=1)Cl","",new Boolean(false)},
+    {"Aromatic mono- and dialkylamine","c[NX3v3]([CH2][CH3])([CH2][CH3])","CCN(CC)C=1C=CC=C(Cl)C=1","",new Boolean(false)},
+    {"Aromatic N-acyl amine","cNC(=O)[#1,CH3]","CC(=O)NC=1C=CC=C(C=1)Cl","NA28ter",new Boolean(false)},
+    {"Aromatic diazo","cN=[N]a","C1=CC=C(C=C1)N=NC=2C=CC=C(C=2)Cl","NA29",new Boolean(false)},
+    {"Biphenyls","c!@c1ccccc1","C1=CC=C(C=C1)C2=CC=CC=C2Cl","",new Boolean(false)},
+    {"Diphenyls","c!@*!@c1ccccc1","c1c(Cl)c(ccc1Cc2ccc(cc2))","",new Boolean(false)},
+    {"Diphenyls","c!@*!@*!@c1ccccc1","c1c(Cl)c(ccc1CCc2ccc(cc2))","",new Boolean(false)}
+*/    
+    protected SMARTSgroups() {
+        super();
+    }
+    
+}

data/Toxtree-v2.6.13/src/mutant/rules/UserInputABUnsaturatedAldehyde.java

@@ -0,0 +1,24 @@
+package mutant.rules;
+
+import toxTree.tree.rules.UserInputRule;
+
+
+public class UserInputABUnsaturatedAldehyde extends UserInputRule {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4030450494902430927L;
+
+	public UserInputABUnsaturatedAldehyde() {
+		super("<html>For a better assessment of a,b unsaturated aldehyde, QSAR calculation could be applied. Would you like to proceed?<br>Warning: the assessment could be time consuming!</html>");
+		setID("Proceed with QSAR13?");
+		setSilentvalue(true);
+	}
+
+	public void removeListener() {
+		this.listener = null;
+		
+	}
+
+}

data/Toxtree-v2.6.13/src/mutant/rules/UserInputAromaticAmine.java

@@ -0,0 +1,47 @@
+/*
+Copyright (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 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.
+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 Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package mutant.rules;
+
+import toxTree.tree.rules.UserInputRule;
+
+public class UserInputAromaticAmine extends UserInputRule {
+	/**
+	 * 
+	 */
+
+	private static final long serialVersionUID = -5385938309932274L;
+
+	public UserInputAromaticAmine() {
+		super("<html>For a better assessment of aromatic amine, QSAR calculation could be applied. Would you like to proceed?<br>Warning: the assessment could be time consuming!</html>");
+		setID("Proceed with QSAR6 and QSAR8?");
+		setSilentvalue(true);
+	}
+	public void removeListener() {
+		this.listener = null;
+		
+	}
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/VerifyAlertsGenotoxic.java

@@ -0,0 +1,42 @@
+/*
+Copyright (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 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.
+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 Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package mutant.rules;
+
+import toxTree.tree.rules.RuleVerifyAlertsCounter;
+
+public class VerifyAlertsGenotoxic extends RuleVerifyAlertsCounter {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -424872251765946518L;
+
+	public VerifyAlertsGenotoxic() {
+		super();
+		setID("Genotoxic alert?");
+		setTitle("At least one alert for genotoxic carcinogenicity fired?");
+	}
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/VerifyAlertsNongenotoxic.java

@@ -0,0 +1,42 @@
+/*
+Copyright (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 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.
+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 Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package mutant.rules;
+
+import toxTree.tree.rules.RuleVerifyAlertsCounter;
+
+public class VerifyAlertsNongenotoxic extends RuleVerifyAlertsCounter {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -424872251765946518L;
+
+	public VerifyAlertsNongenotoxic() {
+		super();
+		setID("Nongenotoxic alert?");
+		setTitle("At least one alert for nongenotoxic carcinogenicity fired?");
+	}
+}
+
+

data/Toxtree-v2.6.13/src/sicret/SicretRules.java

@@ -0,0 +1,357 @@
+/*
+Copyright Ideaconsult Ltd.(C) 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 sicret;
+
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.Observable;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.qsar.DescriptorSpecification;
+
+import toxTree.core.IDecisionInteractive;
+import toxTree.core.IDecisionResult;
+import toxTree.exceptions.DecisionMethodException;
+import toxTree.exceptions.DecisionResultException;
+import toxTree.tree.CategoriesList;
+import toxTree.tree.DecisionNodesList;
+import toxTree.tree.UserDefinedTree;
+
+/**
+ * Decision tree for estimating skin irritation and corrosion potential.
+ * Implements rules publlished in 
+ * <i>The Skin Irritation Corrosion Rules Estimation Tool (SICRET), John D. Walker, Ingrid Gerner, Etje Hulzebos, Kerstin Schlegel, QSAR Comb. Sci. 2005, 24, pp378-384</i>. <br>
+ * <p> Rules: 
+ * <ul>
+ * <li>physicochemical property limits
+ * <li>structural rules 
+ * <li>implementation in {@link sicret.rules} package
+ * </ul>
+ * <p>Categories:
+ * <ul>
+ * <li>{@link sicret.categories.CategoryNotCorrosive}
+ * <li>{@link sicret.categories.CategoryNotIrritatingOrCorrosive}
+ * <li>{@link sicret.categories.CategoryNotIrritating}
+ * <li>{@link sicret.categories.CategoryIrritating}
+ * <li>{@link sicret.categories.CategoryCorrosive}
+ * <li>{@link sicret.categories.CategoryIrritatingOrCorrosive}
+ * <li>{@link sicret.categories.CategoryUnknown} 
+ * </ul>
+ * 
+ * @author Nina Jeliazkova 
+ * @author Martin Martinov 
+ * @version 0.1, 2005-4-30
+ */
+public class SicretRules extends UserDefinedTree implements IDecisionInteractive {
+	/**
+     * Comment for <code>serialVersionUID</code>
+     */
+    private static final long serialVersionUID = 0;
+    protected boolean residuesIDVisible;
+    protected  boolean interactive = true;
+    
+	public final static transient String[] c_rules = { 
+			"sicret.rules.RuleMeltingPoint", //1 Rule1
+			"sicret.rules.RuleLogP",  //2 Rule2
+			"sicret.rules.RuleLipidSolubility", //3 Rule3
+			"sicret.rules.RuleHasOnlyC_H_O", //4 RuleHasOnlyC_H_O
+			"sicret.rules.Rule4", //5 Rule4
+            "sicret.rules.RuleMolWeight", //6 Rule5
+            "sicret.rules.RuleSurfaceTension",  //7 Rule6
+			"sicret.rules.RuleVapourPressure", //8 Rule7
+            "sicret.rules.RuleHasOnlyC_H_O_N", //9 RuleHasOnlyC_H_O_N
+			"sicret.rules.Rule8", //10 Rule8
+			"sicret.rules.Rule9", //11 Rule9
+			"sicret.rules.RuleAqueousSolubility",//12 Rule10
+			"sicret.rules.Rule11",//13 Rule11
+			"sicret.rules.Rule12",//14 Rule12
+			"sicret.rules.Rule13",//15 Rule13
+			"sicret.rules.Rule14", //16 Rule14
+			"sicret.rules.Rule15", //17 Rule15
+			"sicret.rules.Rule16", //18 Rule16
+			"sicret.rules.RuleHasOnlyC_H_O_N_Halogen", //19 RuleHasOnlyC_H_O_N_Halogen
+			"sicret.rules.Rule17",//20 Rule17
+			"sicret.rules.Rule18",//21 Rule18
+			"sicret.rules.Rule19",//22 Rule19
+			"sicret.rules.Rule20",//23 Rule20
+			"sicret.rules.Rule21",//24 Rule21
+			"sicret.rules.Rule22",//25 Rule22
+			"sicret.rules.Rule23",//26 Rule23
+			"sicret.rules.RuleHasOnlyC_H_O_N_S",//27 RuleHasOnlyC_H_O_N_S
+			"sicret.rules.Rule24",  //28 Rule24
+			"sicret.rules.Rule25", //29 Rule25
+			"sicret.rules.Rule26",  //30 Rule26
+			"sicret.rules.Rule27",  //31 Rule27
+			"sicret.rules.Rule28",	//32 Rule28
+			"sicret.rules.RuleHasOnlyC_H_O_Halogen",   //33 RuleHasOnlyC_H_O_Halogen Y/N
+			"sicret.rules.Rule29", //34 Rule29
+			"sicret.rules.Rule30", //35 Rule30
+			"sicret.rules.RuleAlphaAlkynes", //36  //RuleAlphaAlkynes
+			"sicret.rules.RuleHasOnlyC_H_O",//37 RuleHasOnlyC_H_O			
+			"sicret.rules.RuleAcrylicAcids", //38 RuleAcrylicAcids
+			"sicret.rules.RuleOandPQuinones", //39 RuleOandPQuinones
+			"sicret.rules.RuleAliphaticSaturatedAcidsAndHalogenatedAcids",//40 RuleAliphaticSaturatedAcidsAndHalogenatedAcids
+			"sicret.rules.RuleAldehydes",//41 RuleAldehydes
+			"sicret.rules.RulePhenols",//42  RulePhenols
+			"sicret.rules.RuleCatecholsResorcinolsHydroquinones",//43 RuleCatecholsResorcinolsHydroquinones
+			"sicret.rules.RuleCatecholsResorcinolsHydroquinones",//44 RuleCatecholsResorcinolsHydroquinones
+			"sicret.rules.RuleAcidAnhydrides",//45 RuleAcidAnhydrides
+			"sicret.rules.RuleKetenes",//46 RuleKetenes
+			"sicret.rules.RuleBetaLactones",//47 RuleBetaLactones
+			"sicret.rules.RuleLactonesFusedOrUnsaturated",//48 RuleLactonesFusedOrUnsaturated
+			"sicret.rules.RuleEpoxides",//49 RuleEpoxides
+			"sicret.rules.RuleAcrylicAndMethacrylicEsters",//50 RuleAcrylicAndMethacrylicEsters
+			"sicret.rules.RuleKetones",//51 RuleKetones
+			"sicret.rules.RuleC10_C20AliphaticAlcohols",//52 RuleC10_C20AliphaticAlcohols
+			"sicret.rules.RuleEthyleneGlycolEthers",	//53 RuleEthyleneGlycolEthers		
+			"sicret.rules.RuleHydroPeroxides",//54 RuleHydroPeroxides
+			"sicret.rules.RuleHasOnlyC_H_O_N",//55 RuleHasOnlyC_H_O_N
+			"sicret.rules.RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts",//56 RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts
+			"sicret.rules.RuleDi_Tri_Nitrobenzenes",//57 RuleDi_Tri_Nitrobenzenes 
+			"sicret.rules.RuleAlkylAlkanolAmines",//58 RuleAlkylAlkanolAmines
+			"sicret.rules.RuleA_Lactams",//59 RuleA_Lactams 		
+			"sicret.rules.RuleAcidImides",//60 RuleAcidImides 
+			"sicret.rules.RuleAromaticAmines",//61 RuleAromaticAmines
+			"sicret.rules.RuleHasOnlyC_H_O_N_Halogen",//62 RuleHasOnlyC_H_O_N_Halogen
+			"sicret.rules.RuleCarbamoylHalide",//63 RuleCarbamoylHalide
+			"sicret.rules.RuleHalonitrobenzene",//64 RuleHalonitrobenzene
+			"sicret.rules.RuleHasOnlyC_H_O_N_S",//65 RuleHasOnlyC_H_O_N_S
+			"sicret.rules.RuleAlphaHalogenatedAmidesAndThioamides",//66 RuleAlphaHalogenatedAmidesAndThioamides 
+			"sicret.rules.RuleHasOnlyC_H_O_Halogen",//67 RuleHasOnlyC_H_O_Halogen
+			"sicret.rules.RuleBenzylHalides",//68 RuleBenzylHalides
+			"sicret.rules.RuleHalogenatedAlkanesAndAlkenes",//69 //RuleHalogenatedAlkanesAndAlkenes
+			"sicret.rules.RuleTriAndTetraHalogenatedBenzenes"//70//RuleTriAndTetraHalogenatedBenzenes		
+			};
+	private final static transient int c_transitions[][] ={
+		//{if no go to, if yes go to, assign if no, assign if yes}
+		{2,0,0,2}, //Q1 ok
+		{3,0,0,2}, //Q2 ok
+		{4,0,0,1}, //Q3 ok
+		{9,5,0,0}, //Q4 ok
+		{6,0,0,2}, //Q5
+		{7,0,0,1}, //Q6
+		{8,0,0,1}, //Q7
+		{9,0,0,3}, //Q8		 
+		{19,10,0,0}, //Q9 
+		{11,0,0,2}, //Q10
+		{12,0,0,1}, //Q11
+		{13,0,0,1}, //Q12
+		{14,0,0,1}, //Q13
+		{15,0,0,1}, //Q14
+		{16,0,0,3}, //Q15 
+		{17,0,0,3}, //Q16
+		{18,0,0,3}, //Q17  
+		{19,0,0,3}, //Q18
+		{27,20,0,0}, //Q19
+		{21,0,0,2}, //Q20
+		{22,0,0,1}, //Q21
+		{23,0,0,1}, //Q22
+		{24,0,0,1}, //Q23
+		{25,0,0,3}, //Q24		
+		{26,0,0,3}, //Q25
+		{27,0,0,3}, //Q26		
+		{33,28,0,0}, //Q27		
+		{29,0,0,1}, //Q28		
+		{30,0,0,1}, //Q29		
+		{31,0,0,1}, //Q30 		
+		{32,0,0,3}, //Q31 		
+		{33,0,0,3}, //Q32		
+		{36,34,0,0}, //Q33 		
+		{35,0,0,2},  //Q34		
+		{36,0,0,1},  //Q35		
+		{37,0,0,4},  //Q36			
+		{55,38,0,0},  //Q37 		
+		{39,0,0,5},  //Q38 
+		{40,0,0,5},  //Q39 
+		{41,0,0,6},  //Q40
+		{42,0,0,6},   //41
+		{43,0,0,6},   //42
+		{44,0,0,6},   //43
+		{45,0,0,6},   //44
+		{46,0,0,6},   //45
+		{47,0,0,6},   //46
+		{48,0,0,6},   //47
+		{49,0,0,6},   //48
+		{50,0,0,6},   //49
+		{51,0,0,4},   //50
+		{52,0,0,4},   //51
+		{53,0,0,4},   //52
+		{54,0,0,4},   //53
+		{55,0,0,4},   //54
+		{62,56,0,0},  //55		
+		{57,0,0,5},   //56
+		{58,0,0,5},   //57
+		{59,0,0,6},   //58
+		{60,0,0,6},   //59
+		{61,0,0,6},   //60
+		{62,0,0,4},   //61
+		{65,63,0,0},  //62
+		{64,0,0,6},   //63
+		{65,0,0,6},   //64
+		{67,66,0,0},  //65
+		{67,0,0,4},   //66
+		{0,68,7,0},   //67
+		{69,0,0,6},   //68
+		{70,0,0,4},   //69
+		{0,0,7,4}    //70
+	};
+
+	private final static transient String c_categories[] ={
+		"sicret.categories.CategoryNotCorrosive",
+		"sicret.categories.CategoryNotIrritatingOrCorrosive",
+		"sicret.categories.CategoryNotIrritating",
+		"sicret.categories.CategoryIrritating",
+		"sicret.categories.CategoryCorrosive",
+		"sicret.categories.CategoryIrritatingOrCorrosive",
+		"sicret.categories.CategoryUnknown"
+	};
+	/**
+	 * 
+	 */
+	public SicretRules() throws DecisionMethodException {
+		super(new CategoriesList(c_categories),null);
+		rules = new DecisionNodesList(categories,c_rules,c_transitions);
+		if (rules instanceof Observable) ((Observable)rules).addObserver(this);
+		
+		setChanged();
+		notifyObservers();
+		/*
+		if (changes != null ) {
+			changes.firePropertyChange("Rules", rules,null);
+			changes.firePropertyChange("Transitions", transitions,null);
+		}
+		*/
+		setTitle("Skin irritation / skin corrosion");
+
+        setPriority(7);
+	}
+
+
+	/* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#addPropertyChangeListener(java.beans.PropertyChangeListener)
+     */
+    public void addPropertyChangeListener(PropertyChangeListener l) {
+        if (changes == null) 		changes = new PropertyChangeSupport(this);        
+        changes.addPropertyChangeListener(l);
+		for (int i=0; i < rules.size(); i++) 
+			if (rules.getRule(i) != null)
+				rules.getRule(i).addPropertyChangeListener(l);
+    }
+    /* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#removePropertyChangeListener(java.beans.PropertyChangeListener)
+     */
+    public void removePropertyChangeListener(PropertyChangeListener l) {
+        if (changes == null) {
+	        changes.removePropertyChangeListener(l);
+	        for (int i=0; i < rules.size(); i++) 
+	        	if (rules.getRule(i) != null)
+	        		rules.getRule(i).removePropertyChangeListener(l);
+        }	
+    }	
+    /* (non-Javadoc)
+     * @see java.lang.Object#toString()
+     */
+    public String toString() {
+        return getName();
+    }
+	
+	public DescriptorSpecification getSpecification() {
+        return new DescriptorSpecification(
+                "http://toxtree.sourceforge.net/sicret.html",
+                getTitle(),
+                this.getClass().getName(),                
+                "Toxtree plugin");
+	}    
+
+	/* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#getName()
+     */
+    public String getName() {
+        return name;
+    }
+    /* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#setName(java.lang.String)
+     */
+    public void setName(String value) {
+       name = value;
+
+    }
+	public StringBuffer explainRules(IDecisionResult result,boolean verbose) throws DecisionMethodException{
+		try {
+			StringBuffer b = result.explain(verbose);
+			return b;
+		} catch (DecisionResultException x) {
+			throw new DecisionMethodException(x);
+		}
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.tree.AbstractTree#createDecisionResult()
+	 */
+	/*public IDecisionResult createDecisionResult() {
+		IDecisionResult result =  new CramerTreeResult();
+		result.setDecisionMethod(this);
+		return result;
+
+	}*/
+
+
+	public boolean isResiduesIDVisible() {
+		return residuesIDVisible;
+	}
+
+
+	public void setResiduesIDVisible(boolean residuesIDVisible) {
+		this.residuesIDVisible = residuesIDVisible;
+		for (int i=0;i< rules.size(); i++) {
+			rules.getRule(i).hideResiduesID(!residuesIDVisible);
+		}
+	}
+	public void setEditable(boolean value) {
+		editable = value;
+		for (int i=0;i<rules.size();i++)
+			rules.getRule(i).setEditable(value);
+	}
+    @Override
+    public void setParameters(IAtomContainer mol) {
+        if (interactive) {
+            JComponent c = optionsPanel(mol);
+            if (c != null)
+                JOptionPane.showMessageDialog(null,c,"Enter properties",JOptionPane.PLAIN_MESSAGE);
+        }    
+        
+    }
+
+
+    public boolean getInteractive() {
+        return interactive;
+    }
+
+
+
+
+    public void setInteractive(boolean value) {
+        interactive=value;
+        
+    }
+}