toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/MichaelAcceptorRule.java

@@ -0,0 +1,23 @@
+package toxtree.plugins.dnabinding.rules;
+
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+
+
+
+/**
+ * Michael acceptors
+ * @author nina
+ *
+ */
+public class MichaelAcceptorRule extends DNABindingRule {
+
+	public MichaelAcceptorRule() {
+		super(DNABindingAlerts.MICHAEL_ACCEPTORS);
+	}
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6414034762618878368L;
+
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/RuleDNABindingAlerts.java

@@ -0,0 +1,25 @@
+package toxtree.plugins.dnabinding.rules;
+
+import toxTree.tree.rules.RuleInitAlertCounter;
+
+public class RuleDNABindingAlerts extends RuleInitAlertCounter {
+
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5388334940521878939L;
+
+	public RuleDNABindingAlerts() {
+		super();
+		setID("DNA binding alerts");
+		setTitle("Verify structural alerts for DNA binding");
+		setExplanation("");
+		
+	}
+	@Override
+	public boolean isImplemented() {
+		return true;
+	}
+
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/SN1Rule.java

@@ -0,0 +1,20 @@
+package toxtree.plugins.dnabinding.rules;
+
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+
+
+/**
+ * SNAR
+ * @author nina
+ *
+ */
+public class SN1Rule extends DNABindingRule {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -1246232527735694154L;
+
+	public SN1Rule() {
+		super(DNABindingAlerts.SN1);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/SN2Rule.java

@@ -0,0 +1,21 @@
+package toxtree.plugins.dnabinding.rules;
+
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+
+
+/**
+ * SN2
+ * @author nina
+ *
+ */
+public class SN2Rule extends DNABindingRule {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5150275004398569245L;
+
+	public SN2Rule() {
+		super(DNABindingAlerts.SN2);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/ShiffBaseRule.java

@@ -0,0 +1,23 @@
+package toxtree.plugins.dnabinding.rules;
+
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+
+
+
+/**
+ * Shiff base
+ * @author nina
+ *
+ */
+public class ShiffBaseRule extends DNABindingRule {
+
+	public ShiffBaseRule() {
+		super(DNABindingAlerts.SHIFF_BASE);
+	}
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -6764225423440366695L;
+
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/rules/VerifyAlertsDNABinding.java

@@ -0,0 +1,29 @@
+package toxtree.plugins.dnabinding.rules;
+
+import net.idea.modbcum.i.processors.IProcessor;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.renderer.selection.IChemObjectSelection;
+
+import toxTree.tree.rules.RuleVerifyAlertsCounter;
+
+public class VerifyAlertsDNABinding extends RuleVerifyAlertsCounter {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -6848759397201273916L;
+	public VerifyAlertsDNABinding() {
+		super();
+		setID("6");
+		setTitle("At least one alert for DNA binding?");
+	}
+	@Override
+	public boolean isImplemented() {
+		return true;
+	}
+	@Override
+	public IProcessor<IAtomContainer, IChemObjectSelection> getSelector() {
+		return null;
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/func/FuncRules.java

@@ -0,0 +1,649 @@
+/*
+Copyright Istituto Superiore di Sanita' 2009
+
+Contact: rbenigni@iss.it, olga.tcheremenskaia@iss.it, cecilia.bossa@iss.it
+
+
+
+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 toxtree.plugins.func;
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+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.DecisionNodesFactory;
+import toxTree.tree.UserDefinedTree;
+import toxtree.plugins.func.rules.FuncTreeResult;
+
+/**
+ * 
+
+ *
+ */
+public class FuncRules extends UserDefinedTree implements IDecisionInteractive{
+	/**
+     * Comment for <code>serialVersionUID</code>
+     */
+    private static final long serialVersionUID = 0;
+    protected boolean residuesIDVisible;
+ 
+
+    public final static transient String[] c_rules = { 
+        "toxtree.plugins.func.rules.RuleAlertsForFunc", // Rule  1   
+        
+        "toxtree.plugins.func.rules.FG1", //2"
+        "toxtree.plugins.func.rules.FG2", //3        
+        "toxtree.plugins.func.rules.FG3_LS", //4
+        "toxtree.plugins.func.rules.FG3_1", //5
+        "toxtree.plugins.func.rules.FG3_2", //6        
+        "toxtree.plugins.func.rules.FG4_LS", //7
+        "toxtree.plugins.func.rules.FG4_1", //8
+        "toxtree.plugins.func.rules.FG4_2", //9        
+        "toxtree.plugins.func.rules.FG5", //10
+        "toxtree.plugins.func.rules.FG6", //11
+        
+        "toxtree.plugins.func.rules.FG7", //12
+        "toxtree.plugins.func.rules.FG8", //13
+        "toxtree.plugins.func.rules.FG9", //14
+        "toxtree.plugins.func.rules.FG10", //15
+        "toxtree.plugins.func.rules.FG11", //16
+        "toxtree.plugins.func.rules.FG12", //17
+        "toxtree.plugins.func.rules.FG13", //18
+        "toxtree.plugins.func.rules.FG14", //19
+        "toxtree.plugins.func.rules.FG15", //20
+        "toxtree.plugins.func.rules.FG16", //21
+        
+        "toxtree.plugins.func.rules.FG17", //22
+        "toxtree.plugins.func.rules.FG18", //23
+        "toxtree.plugins.func.rules.FG19", //24
+        "toxtree.plugins.func.rules.FG20", //25
+        "toxtree.plugins.func.rules.FG21", //26
+        "toxtree.plugins.func.rules.FG22", //27
+        "toxtree.plugins.func.rules.FG23_LS", //28
+        "toxtree.plugins.func.rules.FG23_1", //29
+        "toxtree.plugins.func.rules.FG23_2", //30
+        "toxtree.plugins.func.rules.FG23_3", //31
+        
+        "toxtree.plugins.func.rules.FG23_4", //32
+        "toxtree.plugins.func.rules.FG23_5", //33
+        "toxtree.plugins.func.rules.FG23_6", //34
+        "toxtree.plugins.func.rules.FG23_7", //35
+        "toxtree.plugins.func.rules.FG23_8", //36
+        "toxtree.plugins.func.rules.FG24_LS", //37
+        "toxtree.plugins.func.rules.FG24_1", //38
+        "toxtree.plugins.func.rules.FG24_2", //39
+        "toxtree.plugins.func.rules.FG24_3", //40     
+        "toxtree.plugins.func.rules.FG25", //41
+        
+        "toxtree.plugins.func.rules.FG26", //42
+        "toxtree.plugins.func.rules.FG27", //43
+        "toxtree.plugins.func.rules.FG28", //44
+        "toxtree.plugins.func.rules.FG29", //45
+        "toxtree.plugins.func.rules.FG30", //46        
+       "toxtree.plugins.func.rules.FG31_LS", //47
+       "toxtree.plugins.func.rules.FG31_1", //48
+       "toxtree.plugins.func.rules.FG31_2", //49
+       "toxtree.plugins.func.rules.FG31_3", //50
+       "toxtree.plugins.func.rules.FG31_4", //51
+       
+       "toxtree.plugins.func.rules.FG31_5", //52
+       "toxtree.plugins.func.rules.FG31_6", //53
+       "toxtree.plugins.func.rules.FG31_7", //54
+       "toxtree.plugins.func.rules.FG31_8", //55
+       "toxtree.plugins.func.rules.FG31_9", //56        
+       "toxtree.plugins.func.rules.FG32", //57        
+       "toxtree.plugins.func.rules.FG33_LS", //58
+       "toxtree.plugins.func.rules.FG33_1", //59
+       "toxtree.plugins.func.rules.FG33_2", //60
+       "toxtree.plugins.func.rules.FG33_3", //61
+       
+       "toxtree.plugins.func.rules.FG33_4", //62
+       "toxtree.plugins.func.rules.FG33_5", //63
+       "toxtree.plugins.func.rules.FG33_6", //64
+       "toxtree.plugins.func.rules.FG33_7", //65
+       "toxtree.plugins.func.rules.FG33_8", //66     
+       "toxtree.plugins.func.rules.FG34_LS", //67
+       "toxtree.plugins.func.rules.FG34_1", //68
+       "toxtree.plugins.func.rules.FG34_2", //69      
+        "toxtree.plugins.func.rules.FG35_LS", //70
+        "toxtree.plugins.func.rules.FG35_1", //71
+        
+        "toxtree.plugins.func.rules.FG35_2", //72
+        "toxtree.plugins.func.rules.FG35_3", //73
+        "toxtree.plugins.func.rules.FG35_4", //74
+        "toxtree.plugins.func.rules.FG35_5", //75
+        "toxtree.plugins.func.rules.FG35_6", //76
+        "toxtree.plugins.func.rules.FG35_7", //77
+        "toxtree.plugins.func.rules.FG35_8", //78
+        "toxtree.plugins.func.rules.FG35_9", //79
+        "toxtree.plugins.func.rules.FG35_10", //80
+        "toxtree.plugins.func.rules.FG35_11", //81
+        
+        "toxtree.plugins.func.rules.FG35_12", //82
+        "toxtree.plugins.func.rules.FG35_13", //83   
+        "toxtree.plugins.func.rules.FG36", //84   
+        "toxtree.plugins.func.rules.FG37_LS", //85
+        "toxtree.plugins.func.rules.FG37_1", //86
+        "toxtree.plugins.func.rules.FG37_2", //87
+        "toxtree.plugins.func.rules.FG37_3", //88
+        "toxtree.plugins.func.rules.FG37_4", //89    
+        "toxtree.plugins.func.rules.FG38", //90
+        "toxtree.plugins.func.rules.FG39", //91
+        
+        "toxtree.plugins.func.rules.FG40", //92    
+        "toxtree.plugins.func.rules.FG41_LS", //93
+        "toxtree.plugins.func.rules.FG41_1", //94
+        "toxtree.plugins.func.rules.FG41_2", //95
+        "toxtree.plugins.func.rules.FG41_3", //96
+        "toxtree.plugins.func.rules.FG41_4", //97
+        "toxtree.plugins.func.rules.FG41_5", //98        
+        "toxtree.plugins.func.rules.FG42", //99
+        "toxtree.plugins.func.rules.FG43", //100
+        "toxtree.plugins.func.rules.FG44", //101
+        
+        "toxtree.plugins.func.rules.FG45", //102    
+        "toxtree.plugins.func.rules.FG46_LS", //103
+        "toxtree.plugins.func.rules.FG46_1", //104
+        "toxtree.plugins.func.rules.FG46_2", //105       
+        "toxtree.plugins.func.rules.FG47", //106        
+        "toxtree.plugins.func.rules.FG48_LS", //107
+        "toxtree.plugins.func.rules.FG48_1", //108
+        "toxtree.plugins.func.rules.FG48_2", //109        
+        "toxtree.plugins.func.rules.FG49", //110        
+        "toxtree.plugins.func.rules.FG50_LS", //111
+        
+        "toxtree.plugins.func.rules.FG50_1", //112
+        "toxtree.plugins.func.rules.FG50_2", //113
+        "toxtree.plugins.func.rules.FG50_3", //114   
+        "toxtree.plugins.func.rules.FG51_LS", //115
+        "toxtree.plugins.func.rules.FG51_1", //116
+        "toxtree.plugins.func.rules.FG51_2", //117
+        "toxtree.plugins.func.rules.FG51_3", //118        
+        "toxtree.plugins.func.rules.FG52_LS", //119
+        "toxtree.plugins.func.rules.FG52_1", //120
+        "toxtree.plugins.func.rules.FG52_2", //121
+        
+        "toxtree.plugins.func.rules.FG52_3", //122        
+        "toxtree.plugins.func.rules.FG53_LS", //123
+        "toxtree.plugins.func.rules.FG53_1", //124
+        "toxtree.plugins.func.rules.FG53_2", //125
+        "toxtree.plugins.func.rules.FG53_3", //126    
+        "toxtree.plugins.func.rules.FG54", //127
+        "toxtree.plugins.func.rules.FG55", //128
+        "toxtree.plugins.func.rules.FG56", //129
+        "toxtree.plugins.func.rules.FG57", //130
+        "toxtree.plugins.func.rules.FG58", //131
+        
+        "toxtree.plugins.func.rules.FG59", //132
+        "toxtree.plugins.func.rules.FG60", //133
+        "toxtree.plugins.func.rules.FG61", //134
+        "toxtree.plugins.func.rules.FG62", //135
+        "toxtree.plugins.func.rules.FG63", //136
+        "toxtree.plugins.func.rules.FG64", //137
+        "toxtree.plugins.func.rules.FG65", //138
+        "toxtree.plugins.func.rules.FG66", //139
+        "toxtree.plugins.func.rules.FG67", //140
+        "toxtree.plugins.func.rules.FG68", //141
+        
+        "toxtree.plugins.func.rules.FG69", //142
+        "toxtree.plugins.func.rules.FG70", //143
+        "toxtree.plugins.func.rules.FG71", //144
+        "toxtree.plugins.func.rules.FG72", //145
+        "toxtree.plugins.func.rules.FG73", //146       
+        "toxtree.plugins.func.rules.FG74_LS", //147
+        "toxtree.plugins.func.rules.FG74_1", //148
+        "toxtree.plugins.func.rules.FG74_2", //149
+        "toxtree.plugins.func.rules.FG74_3", //150
+        "toxtree.plugins.func.rules.FG74_4", //151
+        
+        "toxtree.plugins.func.rules.FG74_5", //152
+        "toxtree.plugins.func.rules.FG74_6", //153
+        "toxtree.plugins.func.rules.FG74_7", //154      
+        "toxtree.plugins.func.rules.FG75_LS", //155
+        "toxtree.plugins.func.rules.FG75_1", //156
+        "toxtree.plugins.func.rules.FG75_2", //157
+        "toxtree.plugins.func.rules.FG75_3", //158
+        "toxtree.plugins.func.rules.FG75_4", //159     
+        "toxtree.plugins.func.rules.FG76", //160
+        "toxtree.plugins.func.rules.FG77", //161
+        
+        "toxtree.plugins.func.rules.FG78_LS", //162
+        "toxtree.plugins.func.rules.FG78_1", //163
+        "toxtree.plugins.func.rules.FG78_2", //164
+        "toxtree.plugins.func.rules.FG78_3", //165
+        "toxtree.plugins.func.rules.FG78_4", //166        
+        "toxtree.plugins.func.rules.FG79_LS", //167
+        "toxtree.plugins.func.rules.FG79_1", //168
+        "toxtree.plugins.func.rules.FG79_2", //169
+        "toxtree.plugins.func.rules.FG79_3", //170
+        "toxtree.plugins.func.rules.FG79_4", //171
+        
+        "toxtree.plugins.func.rules.FG80_LS", //172
+        "toxtree.plugins.func.rules.FG80_1", //173
+        "toxtree.plugins.func.rules.FG80_2", //174   
+        "toxtree.plugins.func.rules.FG81_LS", //175
+        "toxtree.plugins.func.rules.FG81_1", //176
+        "toxtree.plugins.func.rules.FG81_2", //177
+        "toxtree.plugins.func.rules.FG81_3", //178
+        "toxtree.plugins.func.rules.FG81_4", //179       
+        "toxtree.plugins.func.rules.FG82_LS", //180
+        "toxtree.plugins.func.rules.FG82_1", //181
+        
+        "toxtree.plugins.func.rules.FG82_2", //182
+        "toxtree.plugins.func.rules.FG82_3", //183
+        "toxtree.plugins.func.rules.FG82_4", //184        
+        "toxtree.plugins.func.rules.FG83_LS", //185
+        "toxtree.plugins.func.rules.FG83_1", //186
+        "toxtree.plugins.func.rules.FG83_2", //187
+        "toxtree.plugins.func.rules.FG83_3", //188
+        "toxtree.plugins.func.rules.FG83_4", //189        
+        "toxtree.plugins.func.rules.FG84_LS", //190
+        "toxtree.plugins.func.rules.FG84_1", //191
+        
+        "toxtree.plugins.func.rules.FG84_2", //192      
+        "toxtree.plugins.func.rules.FG85", //193
+        "toxtree.plugins.func.rules.FG86", //194
+        "toxtree.plugins.func.rules.FG87", //195
+        "toxtree.plugins.func.rules.FG88", //196
+        "toxtree.plugins.func.rules.FG89", //197
+        "toxtree.plugins.func.rules.FG90", //198
+  
+        
+        
+        "toxTree.tree.rules.RuleVerifyAlertsCounter", //last
+      
+        };
+    private final static transient int c_transitions[][] ={
+        //{if no go to, if yes go to, assign if no, assign if yes}
+        {2,2,0,0}, //Rule 1  1
+        {3,3,0,0}, //2
+        {4,4,0,0}, //3
+        
+        
+        {5,5,0,0}, //4
+        {6,6,0,0}, //5
+        {7,7,0,0}, //6
+        
+        {8,8,0,0}, //7
+        {9,9,0,0}, //8
+        {10,10,0,0}, //9
+        
+        {11,11,0,0}, //10
+        {12,12,0,0}, //11
+        {13,13,0,0}, //12
+        {14,14,0,0}, //13
+        {15,15,0,0}, //14
+        {16,16,0,0}, //15
+        {17,17,0,0}, //16
+        {18,18,0,0}, //17
+        {19,19,0,0}, //18
+        {20,20,0,0}, //19
+        {21,21,0,0}, //20
+        {22,22,0,0}, //21
+        {23,23,0,0}, //22
+        {24,24,0,0}, //23
+        {25,25,0,0}, //24
+        {26,26,0,0}, //25
+        {27,27,0,0}, //26
+        {28,28,0,0}, //27
+        
+        {29,29,0,0}, //28
+        {30,30,0,0}, //29
+        {31,31,0,0}, //30
+        {32,32,0,0}, //31
+        {33,33,0,0}, //32
+        {34,34,0,0}, //33
+        {35,35,0,0}, //34
+        {36,36,0,0}, //35
+        {37,37,0,0}, //36
+        
+        {38,38,0,0}, //37
+        {39,39,0,0}, //38
+        {40,40,0,0}, //39
+        {41,41,0,0}, //40
+        
+        {42,42,0,0}, //41
+        {43,43,0,0}, //42
+        {44,44,0,0}, //43
+        {45,45,0,0}, //44
+        {46,46,0,0}, //45
+        {47,47,0,0}, //46
+        
+        {48,48,0,0}, //47
+        {49,49,0,0}, //48
+        {50,50,0,0}, //49        
+        {51,51,0,0}, //50
+        {52,52,0,0}, //51
+        {53,53,0,0}, //52
+        {54,54,0,0}, //53
+        {55,55,0,0}, //54
+        {56,56,0,0}, //55
+        {57,57,0,0}, //56
+        
+        {58,58,0,0}, //57
+        
+        {59,59,0,0}, //58
+        {60,60,0,0}, //59        
+        {61,61,0,0}, //60
+        
+        
+        {62,62,0,0}, //61
+        {63,63,0,0}, //62
+        {64,64,0,0}, //63
+        {65,65,0,0}, //64
+        {66,66,0,0}, //65
+        {67,67,0,0}, //66
+        
+        {68,68,0,0}, //67
+        {69,69,0,0}, //68
+        {70,70,0,0}, //69
+        
+        
+        {71,71,0,0}, //70
+        {72,72,0,0}, //71
+        {73,73,0,0}, //72
+        {74,74,0,0}, //73
+        {75,75,0,0}, //74
+        {76,76,0,0}, //75
+        {77,77,0,0}, //76
+        {78,78,0,0}, //77
+        {79,79,0,0}, //78
+        {80,80,0,0}, //79        
+        {81,81,0,0}, //80
+        {82,82,0,0}, //81
+        {83,83,0,0}, //82
+        {84,84,0,0}, //83
+        
+        {85,85,0,0}, //84 
+        
+        {86,86,0,0}, //85
+        {87,87,0,0}, //86
+        {88,88,0,0}, //87
+        {89,89,0,0}, //88
+        {90,90,0,0}, //89   
+        
+        {91,91,0,0}, //90
+        {92,92,0,0}, //91
+        {93,93,0,0}, //92
+        
+        {94,94,0,0}, //93
+        {95,95,0,0}, //94
+        {96,96,0,0}, //95
+        {97,97,0,0}, //96
+        {98,98,0,0}, //97
+        {99,99,0,0}, //98
+        
+        {100,100,0,0}, //99        
+        {101,101,0,0}, //100
+        {102,102,0,0}, //101
+        {103,103,0,0}, //102
+        
+        
+        {104,104,0,0}, //103
+        {105,105,0,0}, //104
+        {106,106,0,0}, //105
+        
+        {107,107,0,0}, //106
+        
+        {108,108,0,0}, //107
+        {109,109,0,0}, //108
+        {110,110,0,0}, //109 
+        
+        {111,111,0,0}, //110
+        
+        {112,112,0,0}, //111
+        {113,113,0,0}, //112
+        {114,114,0,0}, //113
+        {115,115,0,0}, //114
+        
+        {116,116,0,0}, //115
+        {117,117,0,0}, //116
+        {118,118,0,0}, //117
+        {119,119,0,0}, //118
+        
+        {120,120,0,0}, //119        
+        {121,121,0,0}, //120
+        {122,122,0,0}, //121
+        {123,123,0,0}, //122
+        
+        {124,124,0,0}, //123
+        {125,125,0,0}, //124
+        {126,126,0,0}, //125
+        {127,127,0,0}, //126
+        
+        
+        {128,128,0,0}, //127
+        {129,129,0,0}, //128
+        {130,130,0,0}, //129       
+        {131,131,0,0}, //130
+        {132,132,0,0}, //131
+        {133,133,0,0}, //132
+        {134,134,0,0}, //133
+        {135,135,0,0}, //134
+        {136,136,0,0}, //135
+        {137,137,0,0}, //136
+        {138,138,0,0}, //137
+        {139,139,0,0}, //138
+        {140,140,0,0}, //139       
+        {141,141,0,0}, //140
+        {142,142,0,0}, //141
+        {143,143,0,0}, //142
+        {144,144,0,0}, //143
+        {145,145,0,0}, //144
+        {146,146,0,0}, //145
+        {147,147,0,0}, //146
+        
+        
+        
+        {149,149,0,0}, //147
+        {149,149,0,0}, //149
+        {150,150,0,0}, //149       
+        {151,151,0,0}, //150
+        {152,152,0,0}, //151
+        {153,153,0,0}, //152
+        {154,154,0,0}, //153
+        {155,155,0,0}, //154
+        
+        
+        {156,156,0,0}, //155
+        {157,157,0,0}, //156
+        {158,158,0,0}, //157
+        {159,159,0,0}, //158
+        {160,160,0,0}, //159
+        
+        {161,161,0,0}, //160
+        {162,162,0,0}, //161
+        
+        {163,163,0,0}, //162
+        {164,164,0,0}, //163
+        {165,165,0,0}, //164
+        {166,166,0,0}, //165
+        {167,167,0,0}, //166
+        
+        {168,168,0,0}, //167
+        {169,169,0,0}, //168
+        {170,170,0,0}, //169        
+        {171,171,0,0}, //170
+        {172,172,0,0}, //171
+        
+        {173,173,0,0}, //172
+        {174,174,0,0}, //173
+        {175,175,0,0}, //174
+        
+        {176,176,0,0}, //175
+        {177,177,0,0}, //176
+        {178,178,0,0}, //177
+        {179,179,0,0}, //178
+        {180,180,0,0}, //179 
+        
+        {181,181,0,0}, //180
+        {182,182,0,0}, //181
+        {183,183,0,0}, //182
+        {184,184,0,0}, //183
+        {185,185,0,0}, //184
+        
+        {186,186,0,0}, //185
+        {187,187,0,0}, //186
+        {188,188,0,0}, //187
+        {189,189,0,0}, //188
+        {190,190,0,0}, //189  
+        
+        {191,191,0,0}, //190
+        {192,192,0,0}, //191
+        {193,193,0,0}, //192
+        
+        {194,194,0,0}, //193
+        {195,195,0,0}, //194
+        {196,196,0,0}, //195
+        {197,197,0,0}, //196
+        {198,198,0,0}, //197
+        {199,199,0,0}, //198
+        
+        
+        {0,0,2,1}, //last
+       
+        
+    };	
+    private final static transient String c_categories[] ={
+		"toxtree.plugins.func.categories.FuncCat1",
+		"toxtree.plugins.func.categories.FuncCat2",
+		
+	};
+	/**
+	 * 
+	 */
+	public FuncRules() throws DecisionMethodException {
+		super(new CategoriesList(c_categories,true),c_rules,c_transitions,new DecisionNodesFactory(true));
+     ;
+		setChanged();
+		notifyObservers();
+		setTitle("Structural Alerts for Functional Group Identification (ISSFUNC)");
+        setPriority(100);
+        setFalseIfRuleNotImplemented(false);};
+        
+    	public DescriptorSpecification getSpecification() {
+            return new DescriptorSpecification(
+                    "http://toxtree.sourceforge.net/issfunc.html",
+                    getTitle(),
+                    this.getClass().getName(),                
+                    "Toxtree plugin");
+    	}
+
+	/* (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();
+        }
+    	
+
+
+    	/* (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);
+    		}
+    	}
+
+
+    	@Override
+    	public IDecisionResult createDecisionResult() {
+    		IDecisionResult result =  new FuncTreeResult();
+    		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 (getInteractive()) {
+                JComponent c = optionsPanel(mol);
+                if (c != null)
+                    JOptionPane.showMessageDialog(null,c,getTitle(),JOptionPane.PLAIN_MESSAGE);
+            } 
+        }
+    }
+
+