toxtree 0.0.1

data/Toxtree-v2.6.13/src/mutant/rules/SA1_gen.java

@@ -0,0 +1,57 @@
+/*
+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.StructureAlertCDK;
+import ambit2.smarts.query.SMARTSException;
+
+public class SA1_gen extends StructureAlertCDK {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 8723199576199214305L;
+
+	public SA1_gen() {
+		super();
+		try {
+			addSubstructure("Acyl halides", "[!$([OH1,SH1])]C(=O)[Br,Cl,F,I]");
+			setID("SA1_gen");
+			setTitle("Acyl halides");
+			setExplanation("Acyl halide RC(=O)[Br,Cl,F,I], where R is not OH or SH.");
+			
+			examples[0] = "O=C(Cl)S";
+			examples[1] = "CN(C)C(=O)Cl";	
+	
+		} catch (SMARTSException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+		}
+	}
+
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/SA20_nogen.java

@@ -0,0 +1,139 @@
+/*
+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 net.idea.modbcum.i.processors.IProcessor;
+
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IRing;
+import org.openscience.cdk.renderer.selection.IChemObjectSelection;
+
+import toxTree.exceptions.DecisionMethodException;
+import toxTree.tree.rules.DefaultAlertCounter;
+import toxTree.tree.rules.IAlertCounter;
+import toxTree.tree.rules.RuleRingSubstituents;
+import toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit;
+
+public class SA20_nogen extends RuleRingSubstituents implements IAlertCounter {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 2801459527105693883L;
+	public static String SA20_title = "(Poly) Halogenated Cycloalkanes (Nongenotoxic carcinogens)";
+	private int ring_halogen_count = 0;
+	private int halogen_count = 0;
+	private final String[] halogens = {"Cl","Br","I","F"};
+	protected IAlertCounter alertsCounter;
+    public SA20_nogen() {
+        super();
+           setID("SA20_nogen");
+            setTitle(SA20_title);
+            setExplanation(SA20_title+"<br>The three halogens have to be directly bound to the same ring.");
+            
+            examples[0] = "[H]C2=C([H])C([H])=C(N=NC1=C([H])C([H])=C(C([H])=C1([H]))N(C([H])([H])[H])C([H])([H])[H])C([H])=C2([H])"; 
+//            	"[H]C1=C([H])C([H])=C2C([H])=C(C([H])=C([H])C2(=C1([H])))N([H])[H]";
+//"C1=CC(=C(C(=C1)Cl)Cl)Cl";
+            examples[1] = "C1CC(C(CC1Br)I)Cl";   
+            editable = false;
+            alertsCounter =  new DefaultAlertCounter();
+            setAnalyzeOnlyRingsWithFlagSet(true);
+            setAnalyzeAromatic(false);
+            setAnalyzeHeterocyclic(false);
+    }
+    public void incrementCounter(IAtomContainer mol) {
+    	alertsCounter.incrementCounter(mol);
+    }
+    
+    @Override
+    public boolean verifyRule(IAtomContainer mol, IAtomContainer selected)
+    		throws DecisionMethodException {
+    	halogen_count = 0;
+    	ring_halogen_count = 0;
+    	if (super.verifyRule(mol,selected)) {
+        	if (halogen_count < ring_halogen_count)
+        		halogen_count = ring_halogen_count;
+
+    		if (halogen_count > 2) {
+    			logger.finer(getID()+"\tHalogens on a single ring\t"+halogen_count);
+	    		incrementCounter(mol);
+	    		return true;
+    		}
+    	}	
+    	return false;
+    }
+    /**
+     * Initialize halogen counts to zero and returns true if the ring consists of single bonds only.
+     */
+    @Override
+    protected boolean analyze(IRing r) {
+    	logger.finer("halogens on a ring\t"+ring_halogen_count);
+    	if (halogen_count < ring_halogen_count)
+    		halogen_count = ring_halogen_count;
+    	ring_halogen_count = 0;
+    	
+    	for (int i =0; i < r.getBondCount(); i++)
+    		if (r.getBond(i).getOrder() != CDKConstants.BONDORDER_SINGLE) return false;
+    	
+    	return true;
+    }
+    /**
+     * Only counts halogens directly connected to the ring and returns true always.
+     */
+	@Override
+	public boolean substituentIsAllowed(IAtomContainer a, int[] place) throws DecisionMethodException {
+		
+		if (a.getAtomCount() == 1)
+			for (int i=0; i < halogens.length; i++) {
+				logger.finer("substituent with atoms\t"+a.getAtom(0).getSymbol());
+				if (halogens[i].equals(a.getAtom(0).getSymbol())) 
+					ring_halogen_count++;
+			}
+		return true;
+	}
+	@Override
+	public String allowedSubstituents() {
+		return "Halogens";
+	}
+	public String getImplementationDetails() {
+		StringBuffer b = new StringBuffer(); 
+		b.append(alertsCounter.getImplementationDetails());
+		b.append("Partitions structure into rings and verifies if there are at least 3 halogens directly bound to the ring.");
+		return b.toString();
+	}
+	@Override
+	public boolean isImplemented() {
+		return true;
+	}
+	
+    @Override
+    public IProcessor<IAtomContainer, IChemObjectSelection> getSelector() {
+    	RuleSMARTSSubstructureAmbit rule = new RuleSMARTSSubstructureAmbit();
+    	try { rule.addSubstructure("[#6;R]!@[Cl,Br,I,F]"); } catch (Exception x) {x.printStackTrace();};
+    	return rule.getSelector();
+    }
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/SA21_gen.java

@@ -0,0 +1,66 @@
+/*
+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 SA21_gen extends StructureAlert {
+	
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -4846012217142617415L;
+	public static String SA21_title = "Alkyl and aryl N-nitroso groups";
+	/**
+	 * TODO
+Please, could you add in this alert also aryl or alkyl substances with the substructure: -N=N-O-H?
+Perhaps with the following MSARTS?
+
+[C,c]N[NX2;v3]=O
+OR 
+[C,c]N=N[OH1]
+
+	 */
+    public SA21_gen() {
+        super();
+        try {
+            addSubstructure(SA21_title, "[C,c]N[NX2;v3]=O");
+            setID("SA21_gen");
+            setTitle(SA21_title);
+            setExplanation(SA21_title);
+            
+            examples[0] = "CCN(CC)N(=O)O";
+            examples[1] = "O=NNCCC";   
+            editable = false;
+        } catch (SMARTSException x) {
+        	logger.log(Level.SEVERE,x.getMessage(),x);
+        }
+    }	
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/SA22_gen.java

@@ -0,0 +1,69 @@
+/*
+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.StructureAlertCDK;
+import ambit2.smarts.query.SMARTSException;
+
+public class SA22_gen extends StructureAlertCDK {
+	
+	                 
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -4104398484154885424L;
+	public static String SA22_title = "Azide and triazene groups";
+	public static String SA22_azide = "Azide";
+	public static String SA22_triazene = "Triazene";
+	
+	public static String SA22_azide_smarts = "[N]=[N]-[N]";
+	public static String SA22_triazene_smarts = "[N]=[N]=[N]";
+	//public static String SA22_azide_triazene_smarts = "[N]=[N]-,=[N]";
+	
+    public SA22_gen() {
+        super();
+        try {
+        	setContainsAllSubstructures(false);
+        	addSubstructure(SA22_azide, SA22_azide_smarts);
+            addSubstructure(SA22_triazene,SA22_triazene_smarts);
+      
+      
+                    	
+            setID("SA22_gen");
+            setTitle(SA22_title);
+            setExplanation(SA22_title);
+            
+            examples[0] = "N=N";
+            examples[1] = "[N-]=[N+]=[N-]";   
+            editable = false;
+        } catch (SMARTSException x) {
+        	logger.log(Level.SEVERE,x.getMessage(),x);
+        }
+    }	                 
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/SA23_gen.java

@@ -0,0 +1,62 @@
+/*
+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.StructureAlertCDK;
+import ambit2.smarts.query.SMARTSException;
+
+public class SA23_gen extends StructureAlertCDK {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -3589707922783454840L;
+	/**
+	 * 
+	 */
+
+	public static String SA23_title = "Aliphatic N-nitro";
+    public SA23_gen() {
+        super();
+        try {
+        	setContainsAllSubstructures(false);
+        	addSubstructure(SA23_title, "[C!r][NH1]N(=O)O");
+        	addSubstructure(SA23_title+"1", "[C!r]N(A)N(=O)O");
+     	
+            setID("SA23_gen");
+            setTitle(SA23_title);
+            setExplanation(SA23_title + "<br>The possibility to have an aromatic substituent on the nitrogen should be excluded.");
+            
+            examples[0] = "CCN(C1=CC=CC=C1)N(=O)O";
+            examples[1] = "CCCN(CC)N(=O)O";   
+            editable = false;
+        } catch (SMARTSException x) {
+        	logger.log(Level.SEVERE,x.getMessage(),x);
+        }
+    }	
+}
+
+

data/Toxtree-v2.6.13/src/mutant/rules/SA24_gen.java

@@ -0,0 +1,60 @@
+/*
+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.StructureAlertCDK;
+import ambit2.smarts.query.SMARTSException;
+
+public class SA24_gen extends StructureAlertCDK {
+	
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5624687406911731732L;
+	public static String SA24_title = "\u03B1,\u03B2 unsaturated alkoxy";
+    public SA24_gen() {
+        super();
+        try {
+        	setContainsAllSubstructures(false);
+        	addSubstructure(SA24_title, "[!$([#6](=O)[!O]),#1][C!H0;!R]([!$([#6](=O)[!O]),#1])!@;=[C!H0;!R]O[#6]");
+        	
+     	
+            setID("SA24_gen");
+            setTitle(SA24_title);
+            setExplanation(SA24_title + "<br>An aromatic substituent on the oxygen is also allowed.<br>If a partial overlap with SA10_gen is found, this alert should not fire.");
+            
+            examples[0] = "COC=CC(C)=O"; //partial overlap with SA10_gen
+//"C1CCC(OC)=CC1";
+            examples[1] = "C=COC=1C=CC(=CC=1)N(=O)O";   
+            editable = false;
+        } catch (SMARTSException x) {
+        	logger.log(Level.SEVERE,x.getMessage(),x);
+        }
+    }		
+}
+
+