toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/plugins/moa/rules/VerifyAlertsUncouplers.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 toxtree.plugins.moa.rules;
+
+import toxTree.tree.rules.RuleVerifyAlertsCounter;
+
+public class VerifyAlertsUncouplers extends RuleVerifyAlertsCounter {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -424872251765946518L;
+
+	public VerifyAlertsUncouplers() {
+		super();
+		setID("Uncouplers alert?");
+		setTitle("At least one alert for Uncouplers fired?");
+	}
+}
+
+

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/ProteinBindingPlugin.java

@@ -0,0 +1,205 @@
+package toxtree.plugins.proteinbinding;
+
+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.proteinbinding.categories.AcylTransferAlerts;
+import toxtree.plugins.proteinbinding.categories.MichaelAcceptors;
+import toxtree.plugins.proteinbinding.categories.NoAlerts;
+import toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts;
+import toxtree.plugins.proteinbinding.categories.SN2Alerts;
+import toxtree.plugins.proteinbinding.categories.SNArAlerts;
+import toxtree.plugins.proteinbinding.categories.ShiffBaseAlerts;
+import toxtree.plugins.proteinbinding.rules.AcylTransferRule;
+import toxtree.plugins.proteinbinding.rules.MichaelAcceptorRule;
+import toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult;
+import toxtree.plugins.proteinbinding.rules.RuleProteinBindingAlerts;
+import toxtree.plugins.proteinbinding.rules.SN2Rule;
+import toxtree.plugins.proteinbinding.rules.SNARRule;
+import toxtree.plugins.proteinbinding.rules.ShiffBaseRule;
+import toxtree.plugins.proteinbinding.rules.VerifyAlertsProteinBinding;
+
+/**
+ * Protein binding
+ * @author nina
+ *
+ */
+public class ProteinBindingPlugin extends UserDefinedTree  implements IDecisionInteractive{
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -8574075125273844906L; 
+
+	   protected boolean residuesIDVisible;
+	    public final static transient String[] c_rules = {
+	    	RuleProteinBindingAlerts.class.getName(),
+	    	SNARRule.class.getName(),
+	    	ShiffBaseRule.class.getName(),
+	    	MichaelAcceptorRule.class.getName(),
+	    	AcylTransferRule.class.getName(),
+	    	SN2Rule.class.getName(),
+	    	VerifyAlertsProteinBinding.class.getName()
+
+	        };
+	    private final static transient int c_transitions[][] ={
+	        //{if no go to, if yes go to, assign if no, assign if yes}
+	        {ProteinBindingAlerts.SNAR.ordinal()+2,ProteinBindingAlerts.SNAR.ordinal()+2,
+        		0,0},
+	        {ProteinBindingAlerts.SHIFF_BASE.ordinal()+2,ProteinBindingAlerts.SHIFF_BASE.ordinal()+2,
+	        		0,ProteinBindingAlerts.SNAR.ordinal()+1},
+	        		
+   	        {ProteinBindingAlerts.MICHAEL_ACCEPTORS.ordinal()+2,ProteinBindingAlerts.MICHAEL_ACCEPTORS.ordinal()+2,
+	        		0,ProteinBindingAlerts.SHIFF_BASE.ordinal()+1},
+	        		
+   	        {ProteinBindingAlerts.ACYL_TRANSFER.ordinal()+2,ProteinBindingAlerts.ACYL_TRANSFER.ordinal()+2,
+	        		0,ProteinBindingAlerts.MICHAEL_ACCEPTORS.ordinal()+1},
+	        		
+   	        {ProteinBindingAlerts.SN2.ordinal()+2,ProteinBindingAlerts.SN2.ordinal()+2,
+	        		0,ProteinBindingAlerts.ACYL_TRANSFER.ordinal()+1},
+
+	        {7,0,0,ProteinBindingAlerts.SN2.ordinal()+1} ,     		
+    	    {0,0,ProteinBindingAlerts.NO_ALERTS.ordinal()+1,0}
+	  
+	    };	
+	    private final static transient String c_categories[] ={
+			SNArAlerts.class.getName(),
+			ShiffBaseAlerts.class.getName(),			
+			MichaelAcceptors.class.getName(),
+			AcylTransferAlerts.class.getName(),
+			SN2Alerts.class.getName(),
+			NoAlerts.class.getName()
+		};
+	    
+		public ProteinBindingPlugin() throws DecisionMethodException {
+	    	super(new CategoriesList(c_categories,true),c_rules,c_transitions,new DecisionNodesFactory(true));
+			
+			setChanged();
+			notifyObservers();
+			/*
+			if (changes != null ) {
+				changes.firePropertyChange("Rules", rules,null);
+				changes.firePropertyChange("Transitions", transitions,null);
+			}
+			*/
+			setTitle("Protein binding Alerts");
+
+	        setPriority(9);
+	        setFalseIfRuleNotImplemented(false);
+	        
+		}
+	    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);
+			}
+		}
+		/* (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 (getInteractive()) {
+	            JComponent c = optionsPanel(mol);
+	            if (c != null)
+	                JOptionPane.showMessageDialog(null,c,"Enter properties",JOptionPane.PLAIN_MESSAGE);
+	        }    
+	        
+	    }
+
+		public DescriptorSpecification getSpecification() {
+	        return new DescriptorSpecification(
+	                "http://toxtree.sourceforge.net/proteinbinding.html",
+	                getTitle(),
+	                this.getClass().getName(),                
+	                "Toxtree plugin");
+		}
+		
+		@Override
+		public IDecisionResult createDecisionResult() {
+			IDecisionResult result =  new ProteinBindingTreeResult();
+			result.setDecisionMethod(this);
+			return result;
+		}
+			
+	
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/ProteinBindingPlugin.properties

@@ -0,0 +1,7 @@
+explanation=Protein binding
+reference1=S. J. Enoch, C. M. Ellison, T. W. Schultz & M. T. D. Cronin, A review of the electrophilic reaction chemistry involved in covalent protein binding relevant to toxicity,Critical Reviews in Toxicology, 2011, 1-20
+uri=http://toxtree.sourceforge.net/proteinbinding.html
+vendor=Ideaconsult Ltd.
+vendoruri=http://www.ideaconsult.net
+priority=9
+endpoint=Protein binding

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/categories/AcylTransferAlerts.java

@@ -0,0 +1,19 @@
+package toxtree.plugins.proteinbinding.categories;
+
+
+
+/**
+ * Acyl transfer
+ * @author nina
+ *
+ */
+public class AcylTransferAlerts extends ProteinBindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 3581691833406315298L;
+	public AcylTransferAlerts() {
+		super(ProteinBindingAlerts.ACYL_TRANSFER);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/categories/MichaelAcceptors.java

@@ -0,0 +1,20 @@
+package toxtree.plugins.proteinbinding.categories;
+
+
+
+/**
+ * Michael Acceptors
+ * @author nina
+ *
+ */
+public class MichaelAcceptors extends ProteinBindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4861205974087430140L;
+	public MichaelAcceptors() {
+		super(ProteinBindingAlerts.MICHAEL_ACCEPTORS);
+	}
+
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/categories/NoAlerts.java

@@ -0,0 +1,26 @@
+package toxtree.plugins.proteinbinding.categories;
+
+
+/**
+ * No alerts
+ * @author nina
+ *
+ */
+public class NoAlerts extends ProteinBindingCategory {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6055850368701920221L;
+	public NoAlerts() {
+		super(ProteinBindingAlerts.NO_ALERTS);
+	}
+	
+	@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.NontoxicCategory;
+	}
+	@Override
+	public CategoryType getNegativeCategoryType() {
+		return CategoryType.ToxicCategory;
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/proteinbinding/categories/ProteinBindingAlerts.java

@@ -0,0 +1,685 @@
+package toxtree.plugins.proteinbinding.categories;
+
+public enum ProteinBindingAlerts {
+	SNAR {
+		@Override
+		public String getCategoryExplanation() {
+			return "Substrate has structural alerts for Nucleophilic Aromatic Substitution.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for SNAr Identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "SNAr-Nucleophilic Aromatic Substitution";
+		}
+		@Override
+		public String getExplanation() {
+			return "identify a potential substrate for Nucleophilic aromatic substitution.";
+		}
+		
+		@Override
+		public String[][] getSMARTS() {
+			return new String[][] {
+					{"SNAr","Activated-benzenes",
+					 "[$(c1([F,Cl,Br,$(OC(F)(F)F),$(C#N)])c([N+](=O)[O-])cc([N+](=O)[O-])cc1),$(c1(F)c([N+](=O)[O-])cc([$([CH]=O),$(C(=O)[CH3]),$(C(F)(F)F)])cc1),$(c1(Cl)c([N+](=O)[O-])cc([CH]=O)cc1),$(c1(F)c([$(C#N),$([CH]=O)])cc([N+](=O)[O-])cc1),$(c1([$(OC(F)(F)F),Br,$(C#N)])c([N+](=O)[O-])cc([CH]=O)cc1),$(c1([F,Cl,Br,$(OC(F)(F)F),$(C#N)])cc([N+](=O)[O-])c([N+](=O)[O-])cc1),$(c1([F,Cl,Br,$(OC(F)(F)F),$(C#N)])c([N+](=O)[O-])cccc1([N+](=O)[O-]))]"
+					},
+					{"SNAr","Activated-poly-fluorobenzenes",
+						 "[$(c1([$([N+](=O)[O-]),$([CH]=O),$(C#N),$(C(=O)[CH3])])c(F)c(F)c(F)c(F)c1(F)),$(c1([$([N+](=O)[O-]),$([CH]=O),$(C#N)])c(F)c(F)c(F)c(F)c1),$(c1([$([N+](=O)[O-]),$([CH]=O),$(C#N)])c(F)c(F)c(F)cc1F),$(c1([$([N+](=O)[O-]),$([CH]=O),$(C#N)])c(F)c(F)cc(F)c1F),$(c1([N+](=O)[O-])c(F)c(F)c(F)cc1),$(c1([N+](=O)[O-])c(F)c(F)cc(F)c1),$(c1([N+](=O)[O-])c(F)c(F)ccc1F),$(c1([N+](=O)[O-])c(F)cc(F)cc1F)]"
+						},
+					{"SNAr","Activated-pyridines",
+						 "[$(c1([F,Cl,Br,$(C#N),$(OC(F)(F)F)])ncc([$(N(=O)=O),$(C#N),$([CH]=O),$(C(=O)[CH3])])cc1),$(c1([F,Cl,Br,$(C#N),$(OC(F)(F)F)])ncccc1[$(N(=O)=O),$(C#N),$([CH]=O),$(C(=O)[CH3])]),$(c1([F,Cl,Br,$(C#N),$(OC(F)(F)F)])ccncc1[$(N(=O)=O),$(C#N),$([CH]=O),$(C(=O)[CH3])])]"
+						}
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"c1(Cl)ncncc1":"C";
+		}		
+		@Override
+		public String getShortName() {
+			return "SNAR";
+		}
+	},	
+	SHIFF_BASE {
+		@Override
+		public String getCategoryExplanation() {
+			return "Identified a structural alert or precursor for shiff base formation.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for Schiff base formation  identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "Schiff Base Formation";
+		}
+		@Override
+		public String getExplanation() {
+			return "to be a potential substrate for Schiff base formation.";
+		}
+		@Override
+		public String[][] getSMARTS() {
+			return new String[][] {
+					{
+					"Direct-acting-Schiff-base-formers",	
+					"Mono-aldehydes",
+					"[CH2,$([CH](=O)[CX4]),$([CH](=O)c1a(*)caaa1),$([CH](=O)c1a(*)aaa1)]=O"
+					},
+					{
+					"Direct-acting-Schiff-base-formers",
+					"Disubstituted-polarised-aldehydes",
+					"[$(C(=C)([#6])[#6]);!$(C(=C)([#6])C=[CH2,CH])]=C[CH]=O"
+					},	
+					{
+					"Direct-acting-Schiff-base-formers",
+					"1,2-Dicarbonyl",
+					"[CH,$(C(=O)(C=O)[CX4]),$(C(=O)(C=O)c1a(*)aaaa1),$(C(=O)(C=O)c1a(*)aaa1)](=O)[CH,$(C(=O)(C=O)[#6]);!$(C(=O)(C=O)C=[CH2,CH]);!$(C(=O)(C=O)C#C)]=O"
+					},
+					{
+					"Direct-acting-Schiff-base-formers",
+					"1,3-Dicarbonyl",
+					"[CH,$(C(=O)([CX4]C=O)[CX4]),$(C(=O)([CX4]C=O)c1a(*)aaaa1),$(C(=O)([CX4]C=O)c1a(*)aaa1)](=O)[CX4][CH,$(C(=O)([CX4]C=O)[#6]);!$(C(=O)([CX4]C=O)C=[CH2,CH]);!$(C(=O)([CX4]C=O)C#C)]=O"
+					},
+					{
+					"Pro-Schiff-base-formers-(glyoxal)",
+					"Ethylenediamines",
+					"[$([NH2,$([NH]([CH2])[CX4])][CH2][CH2][NH2]),$([NH]1[CH2][CH2][NH][CH2][CH2]1)]"
+					},						
+					{
+					"Pro-Schiff-base-formers-(glyoxal)",
+					"Ethanolamines",
+					"[$([NH2,$([NH]([CH2])[CX4])][CH2][CH2][OH]),$([NH]1[CH2][CH2]O[CH2][CH2]1)]"
+					},	
+					{
+					"Pro-Schiff-base-formers-(mono-aldehydes)",	
+					"Pro-disubstituted-polarised-aldehydes (disubstituted allyl alcohols)",
+					"C([#6])([#6])=[CH,$(C(=C)([CH2][OH])[#6])][CH2][OH]"
+					},						
+					
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"[CH2]=O":"C";
+		}
+		@Override
+		public String getShortName() {
+			return "SB";
+		}
+	},
+
+	MICHAEL_ACCEPTORS {
+		@Override
+		public String getCategoryExplanation() {
+			return "A structural alert has been identified for a potential Michael Acceptor or michael acceptor precursor.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for Michael Acceptor identified.";
+		}
+		@Override
+		public String getExplanation() {
+			return "to be a potential Michael reaction acceptor or a precursor.";
+		}
+		@Override
+		public String getTitle() {
+			return "Michael Acceptor";
+		}
+		@Override
+		public String[][] getSMARTS() {
+			return new String[][] {
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-aldehydes",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][CH]=O"
+					},
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-ketones",
+					"[$([$([CH2]),$([CH][#6])]=[CH,$(C[#6])]C(=O)[#6]);!$([CH]1=CC(=O)C=CC1(=O));!$([CH]1=CC(=O)C(=O)C=C1)]"
+					},			
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-esters",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]C(=O)O[#6]"
+					},
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-amides",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]C(=O)[NH2,$([NH](C=O)[#6]),$(N(C=O)([#6])[#6])]"
+					},			
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-nitros",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][N+](=O)[O-]"
+					},		
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-cyano",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]C#N"
+					},		
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-sulfonate",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]S(=O)(=O)O[#6]"
+					},	
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-sulfone",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]S(=O)(=O)[#6]"
+					},			
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-sulfinyl",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][SX3](=O)[#6]"
+					},			
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-oximes",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][SX3](=O)[#6]"
+					},	
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-pyridines",
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][$(c1ncccc1),$(c1ccncc1)]"
+					},	
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-pyrazines", //12
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])]c1nccnc1"
+					},	
+					{
+					"Polarised-alkenes",
+					"Polarised-alkene-pyrimidines", //13
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][$(c1ncncc1),$(c1ncccn1),$(c1cncnc1)]"
+					},		
+					{
+					"Polarised-alkenes",
+					"Polarised-akene-triazines", //14
+					"[$([CH2]),$([CH][#6])]=[CH,$(C[#6])][$(c1ncncn1),$(c1nncnc1),$(c1nnccn1),$(c1cnncn1),$(c1nnncc1),$(c1cnnnc1)]"
+					},	
+					{
+					"Polarised-azo-compounds",
+					"Azocarbonamides", //15
+					"[NH2,$([NH](C=O)[#6]),$(N(C=O)([#6])[#6])]C(=O)N=NC(=O)[NH2,$([NH](C=O)[#6]),$(N(C=O)([#6])[#6])]"
+					},		
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-aldehydes", //16
+					"[CH,$(C(#C)[#6])]#C[CH]=O"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-ketones", //17
+					"[CH,$(C(#C)[#6])]#CC(=O)[#6]"
+					},
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-esters", //18
+					"[CH,$(C(#C)[#6])]#CC(=O)O[#6]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-amides", //19
+					"[CH,$(C(#C)[#6])]#CC(=O)[$([NH2]),$([NH](C=O)[#6]),$(N(C=O)([#6])[#6])]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-nitros", //20
+					"[CH,$(C(#C)[#6])]#C[N+](=O)[O-]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-cyano", //21
+					"[CH,$(C(#C)[#6])]#CC#N"
+					},		
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-sulfonate", //22
+					"[CH,$(C(#C)[#6])]#CS(=O)(=O)O[#6]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-sulfone", //23
+					"[CH,$(C(#C)[#6])]#CS(=O)(=O)[#6]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-sulfinyl", //24
+					"[CH,$(C(#C)[#6])]#C[SX3](=O)[#6]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-pyridines", //25
+					"[CH,$(C(#C)[#6])]#C[$(c1ncccc1),$(c1ccncc1)]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-pyrazine", //26
+					"[CH,$(C(#C)[#6])]#Cc1nccnc1"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-pyrimidine", //27
+					"[CH,$(C(#C)[#6])]#C[$(c1ncccn1),$(c1cncnc1),$(c1ncncc1)]"
+					},	
+					{
+					"Polarised-alkynes",
+					"Polarised-alkyne-triazines", //28
+					"[CH,$(C(#C)[#6])]#C[$(c1ncncn1),$(c1nncnc1),$(c1nnccn1),$(c1cnncn1)]"
+					},	
+					{
+					"Quinones-and-quinone-type-chemicals",
+					"Quinones", //29
+					"[$(C1(=O)[#6]=,:[#6]C(=O)[CH]=C1),$(C1(=O)C(=O)[#6]=,:[#6][CH]=C1)]"
+					},	
+					{
+					"Quinones-and-quinone-type-chemicals",
+					"Quinone-methides", //30
+					"[$(C1=CC(=O)[#6]=,:[#6]C1(=[CH][CX4])),$(C1(=[CH][CX4])C(=O)[#6]=,:[#6]C=C1)]"
+					},		
+					{
+					"Quinones-and-quinone-type-chemicals",
+					"Quinone-imines", //31
+					"[$(C1(=O)[#6]=,:[#6][$(C=[NH]),$(C=N[CX4])][CH]=C1),$(C1(=O)[$(C=[NH]),$(C=N[CX4])][#6]=,:[#6][CH]=C1),$(C1(=O)[$(C=[NH]),$(C=N[CX4])]C=[CH][#6]=,:[#6]1)]"
+					},			
+					{
+					"Quinones-and-quinone-type-chemicals",
+					"Quinone-diimines", //32
+					"[$([CH]1=C[$(C=[NH]),$(C=N[CX4])][#6]=,:[#6][$(C=[NH]),$(C=N[CX4])]1),$([CH]1=C[$(C=[NH]),$(C=N[CX4])][$(C=[NH]),$(C=N[CX4])][#6]=,:[#6]1)]"
+					},	
+					{
+					"Quinones-and-quinone-type-chemicals",
+					"Pyranones", //33
+					"[$([cH]1cc(=[O,NH])cc[o,n]1),$([cH]1cc(=[O,NH])[o,n]cc1),$(c1cc(=[O,NH])[o,n][cH]c1)]"
+					},	
+					{
+					"Acid-imides",
+					"Acid-imides", //34
+					"O=C1[NH,$(N(C=O)(C=O)[#6])]C(=O)[CH,$(C(C=O)(=C)[#6])]=[CH]1"
+					},	
+					{
+					"Pre-quinones-and-quinone-type-chemicals",
+					"Hydroquinones", //35
+					"[$(c1([OH,$(O[CH3])])c[cH]c([OH,$(O[CH3])])cc1),$(c1([OH,$(O[CH3])])c([OH,$(O[CH3])])cc[cH]c1)]"
+					},		
+					{
+					"Pre-quinones-and-quinone-type-chemicals",
+					"Alkyl-phenols", //36
+					"[$(c1([OH])ccc([CH3,$([CH2][CX4])])cc1),$(c1([OH])c([CH3,$([CH2][CX4])])cccc1)]"
+					},	
+					{
+					"Pre-quinones-and-quinone-type-chemicals",
+					"Aminophenols", //37
+					"[$(c1([OH])c[cH]c([NH2])cc1),$(c1([OH])c([NH2])cc[cH]c1)]"
+					},
+					{
+					"Pre-quinones-and-quinone-type-chemicals",
+					"Benzenediamines", //38
+					"[$(c1([NH2])c[cH]c([NH2])cc1),$(c1([NH2])c([NH2])cc[cH]c1)]"
+					},
+															{
+					"Pre-polarised-alkenes",
+					"Pre-polarised-alkenes-aldehydes (allyl alcohols)", //39
+					"[CH2,$([CH](=C)[#6])]=[CH,$(C(=C)([CH2][OH])[#6])][CH2][OH]"
+					},
+															{
+					"Pre-polarised-alkynes",
+					"Pre-polarised-alkynes-aldehydes (propargyl alcohols)", //40
+					"[CH,$(C(#C)[#6])]#C[CH2][OH]"
+					},					
+			};
+					
+		}
+		
+		@Override
+		public String getExample(boolean value) {
+			return value?"[OH]c1cccc2ccccc12":"C";
+		}
+		@Override
+		public String getShortName() {
+			return "MA";
+		}
+	},
+	ACYL_TRANSFER {
+		@Override
+		public String getCategoryExplanation() {
+			return "A structural alert for an acyl transfer agent, or a precursor, was identified.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for Acyl Transfer agent identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "Acyl Transfer Agents";
+		}
+		@Override
+		public String getExplanation() {
+			return "identifies a potential acyl transfer agent or precursor.";
+		}
+		@Override
+		public String[][] getSMARTS() {
+			return new String[][] {
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Acyl-halides", //1
+					 "[#6,#1]C(=O)[F,Cl,Br,I]"
+					},
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Acetates", //2
+					 "[#6,#1]C(=[O,SX2])[O,SX2,NX3][$([a;r6]),$([a;r5]),$(C([O,SX2,NX3])=C),$(C([O,SX2,NX3])#C)]"
+					},
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Anhydrides", //3
+					 "[#6,#1]C(=[O,SX2])[O,SX2]C(=[O,SX2])[#6,#1]"
+					},
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Azlactones", //4
+					 "C1=[O,SX2,NX2,CX3]CC(=[O,SX2])[O,SX2,NX3]1"
+					},
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Sulphonyl-halides", //5
+					 "[#6,#1]S(=O)(=O)[F,Cl,Br,I,$(C#N)]"
+					},		
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Phosphonic-acid-halides", //6
+					 "[#6]OP(=O)(O[#6])[F,Cl,Br,I,$(C#N)]"
+					},
+					{"Direct-acylation-involving-a-leaving-group",
+					 "Dialkyl-carbamyl-halides", //7
+					 "N([#6])([#6])C(=O)[F,Cl,Br,I]"
+					},
+					{"Ring-opening-acylation",
+						 "b-Lactones", //8
+						 "C1C(=O)OC1"
+					},
+					{"Ring-opening-acylation",
+						 "Thio-lactones", //9
+						 "C1C(=O)SC1"
+					},
+					{"Ring-opening-acylation",
+						 "a-Lactams", //10
+						 "C1C(=O)NC1"
+					},		
+					{"Ring-opening-acylation",
+						 "Cyclopropenones", //11
+						 "C1([#6,#1])=C([#6,#1])C1(=O)"
+					},	
+					{"Isocyanates-and-related",
+						 "Isocyanates", //12
+						 "[#6,#1]N=C=O"
+					},
+					{"Isocyanates-and-related",
+						 "Isothiocyanates", //13
+						 "[#6,#1]N=C=S"
+					},		
+					{"Isocyanates-and-related",
+						 "Dithiocarbonamide-acid-esters", //14
+						 "[#6]N=C(S[#6])S[#6]"
+					},
+					{"Isocyanates-and-related",
+						 "Carbodiimides", //15
+						 "[#6]N=C=N[#6]"
+					},		
+					{"Isocyanates-and-related",
+						 "Ketenes", //16
+						 "C([#6,#1])([#6,#1])=C=O"
+					}					
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"Cc1oc2ccccc2n1":"C";
+		}
+		@Override
+		public String getShortName() {
+			return "acyl";
+		}
+	},
+	SN2 {
+		@Override
+		public String getCategoryExplanation() {
+			return "Structural Alert Identified for potential second order nucleophilic aliphatic substitution reaction.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for SN2 identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "SN2-Nucleophilic Aliphatic Substitution";
+		}
+		@Override
+		public String getExplanation() {
+			return "to be a substrate for second-order nucleophilic substitution, or a precursor for it.";
+		}
+		@Override
+		public String[][] getSMARTS() {
+			return new String[][] {
+					{"Epoxides-and-related",
+						 "Epoxides", //1
+						 "C1OC1"
+					},
+					{"Epoxides-and-related",
+						 "Aziridines", //2
+						 "C1[NX3]C1"
+					},			
+					{"Epoxides-and-related",
+						 "Sulfaranes", //3
+						 "C1[SX2]C1"
+					},
+					{"Epoxides-and-related",
+						 "Epoxypropane", //
+						 "C1[CH2,CH]OC1"
+					},	
+					{"Epoxides-and-related",
+						 "Epithiopropane", //
+						 "C1[CH2,CH][SX2]C1"
+					},
+					{"Ring-opening-SN2-reaction",
+						 "Lactones", //4
+						 "C1CC(=O)O1"
+					},		
+					{"SN2-reaction-at-a-nitrogen-atom",
+						 "Nitrosoureas-(nitrogen)", //5
+						 "[NX3]C(=O)[$([NH](C=O)[NX2]=O),$(N(C=O)([#6])[NX2]=O)]"
+					},		
+					{"SN2-reaction-at-a-nitrogen-atom",
+						 "Nitrosoguanidine-(nitrogen)", //6
+						 "[NX3]C(=[NH])[$([NH](C=[NH])[NX2]=O),$(N(C=[NH])([#6])[NX2]=O)]"
+					},	
+					{"SN2-reaction-at-a-nitrogen-atom",
+						 "N-acetoxy-N-acetyl-phenyl", //7
+						 "[a][NX3](O[$([CH](O)=O),$(C(=O)(O)[#6])])[$([CH](N)=O),$(C(=O)(N)[#6])]"
+					},	
+					{"SN2-reaction-at-a-nitrogen-atom",
+						 "N-acyloxy-N-alkoxyamides", //8
+						 "[#6]O[NX3](O[$([CH](O)=O),$(C(=O)(O)[#6])])[$([CH](N)=O),$(C(=O)(N)[#6])]"
+					},	
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Isothiazol-3-ones-(sulphur)", //9
+						 "[cH,$(c(c)([sX2])[#6])]1[cH,$(c(c)(c=O)[#6])]c(=O)[nH,$(n(c=O)([sX2])[#6])][sX2]1"
+					},		
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Isothiazolin-3-ones-(sulphur)", //10
+						 "[CH2,$([CH](C)([SX2])[#6])]1[CH2,$([CH](C)(C=O)[#6])]C(=O)[NH,$(N(C=O)([SX2])[#6])][SX2]1"
+					},	
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "aromatic-sulphonic-acids", //11
+						 "[a][SX3](=O)[OH]"
+					},				
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Thiocyanates", //12
+						 "[#6][SX2]C#N"
+					},		
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Thiols", //13
+						 "[#6][SH]"
+					},	
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Disulfides", //14
+						 "[#6][SX2][SX2][#6]"
+					},	
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Thiosulfonates", //15
+						 "[#6][SX2][SX2][#6]"
+					},		
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Sulfoxides-of-disulfides", //16
+						 "[#6][SX2][SX4](=O)(=O)[#6]"
+					},	
+					{"SN2-reaction-at-a-sulphur-atom",
+						 "Sulfenyl-halides", //17
+						 "[#6][SX2][F,Cl,Br,I]"
+					},		
+					/* SN2-reaction-at-a-halo-atom  */ 
+					{"SN2-reaction-at-a-halo-atom",
+						 "N-chloro-sulphonamides", //18
+						 "[#6][SX4](=O)(=O)[NH]Cl"
+					},	
+					{"SN2-reaction-at-a-halo-atom",
+						 "N-haloimides", //19
+						 "[CH,$(C(=O)(N)[#6])](=O)[NX3]([F,Cl,Br,I])[CH,$(C(=O)(N)[#6])]=O"
+					},	
+					/* SN2-reaction-at-a-sp2-carbon  */ 
+					{"SN2-reaction-at-a-sp2-carbon",
+						 "Polarised-alkenes-with-a-halogen-leaving-group", //20
+						 "C=[CH][F,Cl,Br,I]"
+					},	
+					{"SN2-reaction-at-a-sp2-carbon",
+						 "Polarised-alkenes-with-a-sulfonate-leaving-group", //21
+						 "C=[CH]OS(=O)(=O)[#6]"
+					},	
+					{"SN2-reaction-at-a-sp2-carbon",
+						 "Polarised-alkenes-with-a-sulfate-leaving-group", //22
+						 "C=[CH]OS(=O)(=O)O[#6]"
+					},	
+					{"SN2-reaction-at-a-sp2-carbon",
+						 "Polarised-alkenes-with-a-phosphonate-leaving-group", //23
+						 "C=[CH]OP(=[O,SX])(O[#6])[#6]"
+					},	
+					{"SN2-reaction-at-a-sp2-carbon",
+						 "Polarised-alkenes-with-a-phosphate-leaving-group", //24
+						 "C=[CH]OP(=[O,SX])(O[#6])O[#6]"
+					},	
+					/* Episulfonium-ion-formation  */ 
+					{"Episulfonium-ion-formation",
+						 "Mustards", //25
+						 "[NX3,SX2][CH2,$([CH]([NX3,SX2])([CX4])[CX4])][CH2,$([CH]([CX4])([Cl,Br,I])[CX4])][Cl,Br,I]"
+					},			
+					{"Episulfonium-ion-formation",
+						 "1,2-Dihaloalkanes", //26
+						 "[Cl,Br,I][CH2,$([CH]([Cl,Br,I])([CX4])[CX4])][CH2,$([CH]([Cl,Br,I])([CX4])[CX4])][Cl,Br,I]"
+					},
+					/* SN2-at-an-sp3-carbon-atom  */ 
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Aliphatic-halide", //27
+						 "[CH3,$([CH2]([F,Cl,Br,I])[#6]),$([CH]([F,Br,Cl,I])([#6])[#6]);!$([CH2,CH]C=O);!$([CH2,CH][CX4][NX3,SX2]);!$([CH2,CH][CX4][F,Cl,Br,I])][F,Cl,Br,I]"
+					},						
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Sulfates", //28
+						 "[#6]OS(=O)(=O)O[CH3,$([CH2](O)[#6]),$([CH](O)([#6])[#6])]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Sulfonates", //29
+						 "[#6]S(=O)(=O)O[CH3,$([CH2](O)[#6]),$([CH](O)([#6])[#6])]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Allyl-acetates-and-related", //30
+						 "[#6]C(=[O,SX1])[O,SX2][CH2,$([CH]([O,SX2])[#6])][c,CX3,CX2]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Nitrosoureas-(carbon)", //31
+						 "[NH2,$([NH](C=[O,NH])[#6]),$(N(C=[O,NH])([#6])[#6])]C(=[O,NH])[NX3]([NX2]=O)[CH3,$([CH2](N)[#6]),$([CH](N)([#6])[#6])]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "a-Halocarbonyls", //32
+						 "[$([CH]=[O,SX1]),$(C([#6])=[O,SX1])][CH2,$([CH](C=[O,SX1])[#6])][F,Cl,Br,I]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Phopshates-(inc-thiophosphates)", //33
+						 "[#6][O,SX2]P(=[O,SX1])([O,SX2][#6])[O,SX2][CH3,$([CH2](O)[#6]),$([CH](O)([#6])[#6])]"
+					},						
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Phosphonates-(inc-thiophosphonates)", //34
+						 "[#6][O,SX2]P(=[O,SX1])([#6])[O,SX2][CH3,$([CH2](O)[#6]),$([CH](O)([#6])[#6])]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "a-Haloethers", //35
+						 "[CX4]O[CH2,$([CH](O)([F,Cl,Br,I])[#6])][F,Cl,Br,I]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "b-Haloethers", //36
+						 "[CX4]O[CH2,$([CH](O)([CX4])[CX4]),$(C(O)([CX4])([CX4])[CX4])][CH2,$([CH](O)([F,Cl,Br,I])[#6])][F,Cl,Br,I]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "Alkyl-diazo", //37
+						 "[CH3,$([CH2](N=N)[#6]),$([CH](N=N)([#6])[#6])][NX2]=[NH,$(N(=N)[#6])]"
+					},	
+					{"SN2-at-an-sp3-carbon-atom",
+						 "a-Haloalkenes", //38
+						 "[CH2,$([CH](=C)[#6]),$(C(=C)([#6])[#6])]=[CH,$(C(=C)[#6])][$([CH2](C=C)[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])]),$([CH](C=C)([#6])[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])])]"
+					},
+					{"SN2-at-an-sp3-carbon-atom",
+						 "a-Haloalkynes", //39
+						 "[CH,$(C(#C)[#6])]#C[$([CH2](C#C)[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])]),$([CH](C#C)([#6])[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])])]"
+					},		
+					{"SN2-at-an-sp3-carbon-atom",
+						 "a-Halobenzyls", //40
+						 "[c][$([CH2]([c])[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])]),$([CH]([a])([#6])[F,Cl,Br,I,$(C#N),$(OS(=O)(=O)O[#6]),$(OS(=O)(=O)[#6])])]"
+					},							
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"c1ccc2cc3ccccc3cc2c1":"C";
+		}
+		@Override
+		public String getShortName() {
+			return "SN2";
+		}
+	},
+	NO_ALERTS {
+		@Override
+		public String getCategoryExplanation() {
+			return "No structural alerts have been identified.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "No protein binding alerts identified.";
+		}
+		@Override
+		public String getTitle() {
+			return getTitle();
+		}
+		@Override
+		public String getExplanation() {
+			return getCategoryExplanation();
+		}
+		@Override
+		public String[][] getSMARTS() {
+			return null;
+		}
+		@Override
+		public String getExample(boolean arg0) {
+			return null;
+		}
+		@Override
+		public String getShortName() {
+			return "Non";
+		}
+	};
+	public String getID() {
+		return toString();
+	}
+	public abstract String getTitle();
+	public abstract String getExplanation();
+	public abstract String getCategoryTitle();
+	public abstract String getCategoryExplanation();
+	public abstract String[][] getSMARTS();
+	public abstract String getExample(boolean value);
+	public abstract String getShortName();
+	
+}