toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/SkinSensitisationPlugin.properties

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+explanation=Identification of mechanisms of toxic action for skin sensitisation using a SMARTS pattern based approach
+reference1=Enoch SJ, Madden JC, Cronin MT,Identification of mechanisms of toxic action for skin sensitisation using a SMARTS pattern based approach.,SAR QSAR Environ Res. 2008;19(5-6):555-78
+uri=http://toxtree.sourceforge.net/skinsensitisation.html
+vendor=Procter&Gamble
+vendoruri=http://pg.com
+priority=9
+endpoint=Skin Sensitisation

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

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * Acyl transfer
+ * @author nina
+ *
+ */
+public class AcylTransferAlerts extends SkinSensitisationCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 3581691833406315298L;
+	public AcylTransferAlerts() {
+		super(SkinSensitisationAlerts.ACYL_TRANSFER);
+	}
+}

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

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * Michael Acceptors
+ * @author nina
+ *
+ */
+public class MichaelAcceptors extends SkinSensitisationCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4861205974087430140L;
+	public MichaelAcceptors() {
+		super(SkinSensitisationAlerts.MICHAEL_ACCEPTORS);
+	}
+}

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

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * No alerts
+ * @author nina
+ *
+ */
+public class NoAlerts extends SkinSensitisationCategory {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6055850368701920221L;
+	public NoAlerts() {
+		super(SkinSensitisationAlerts.NO_ALERTS);
+	}
+	
+	@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.NontoxicCategory;
+	}
+	@Override
+	public CategoryType getNegativeCategoryType() {
+		return CategoryType.ToxicCategory;
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/categories/SN2Alerts.java

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * second order nucleophilic aliphatic substitution reaction
+ * @author nina
+ *
+ */
+public class SN2Alerts extends SkinSensitisationCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -3176004732905640400L;
+
+	public SN2Alerts() {
+		super(SkinSensitisationAlerts.SN2);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/categories/SNArAlerts.java

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * Substrate has structural alerts for Nucleophilic Aromatic Substitution
+ * @author nina
+ *
+ */
+public class SNArAlerts extends SkinSensitisationCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5734136598332428372L;
+
+	public SNArAlerts() {
+		super(SkinSensitisationAlerts.SNAR);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/categories/ShiffBaseAlerts.java

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+package toxtree.plugins.skinsensitisation.categories;
+
+
+/**
+ * Shiff base
+ * @author nina
+ *
+ */
+public class ShiffBaseAlerts extends SkinSensitisationCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6055850368701920221L;
+	public ShiffBaseAlerts() {
+		super(SkinSensitisationAlerts.SHIFF_BASE);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/categories/SkinSensitisationAlerts.java

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+package toxtree.plugins.skinsensitisation.categories;
+
+public enum SkinSensitisationAlerts {
+	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[] {
+					"c1([F,Cl,Br,I,$(N(=O)~O)])c([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])cc([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])cc1",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])c([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])cccc1([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])ncc([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])cc1",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])ncccc1([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])ncccn1",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])ncncc1",
+					"c1([F,Cl,Br,I,$(N(=O)~O)])ncc([F,Cl,Br,I,$(N(=O)~O),$(C#N),$(C=O),$(C(F)(F)F),$(S=O)])nc1",
+					"c1nc([F,Cl,Br,I,$(N(=O)~O)])ncn1"
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"c1(Cl)ncncc1":"C";
+		}		
+		@Override
+		public String getShortName() {
+			return "SNAR";
+		}
+	},	
+	SHIFF_BASE {
+		@Override
+		public String getCategoryExplanation() {
+			return "Identified a structural alert or precursor for shiff base formation.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for Schiff base formation  identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "Schiff Base Formation";
+		}
+		@Override
+		public String getExplanation() {
+			return "to be a potential substrate for Schiff base formation.";
+		}
+		@Override
+		public String[] getSMARTS() {
+			return new String[] {
+				"[CH2]=O",
+				"[CH2]N([CH3])[CH3]",
+				"CC(C)=[CH][CH2][OH]",
+				"CC=C(C)[CH2][OH]",
+				"[CX4][CH]=[O,SX2]",
+				"[a][CH]=O",
+				"C(C)(C)=CC=[O,SX2]",
+				"[C;!r5]([C;!r5])=[C;!r5](C)[C;!r5]=[O,SX2;!r5]",
+				"[#6]C(=[O,SX2])C(=[O,SX2])[#6]",
+				"[#6]C(=[O,SX2])[CX4]C(=[O,SX2])[#6]",
+				"[#6][$([NX2]=O),$(N=C=O),$(OC#N),$(SC#N),$(N=C=S)]",
+				"[CH2][NH2+0]"
+			};
+		}
+		@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[] {
+				"[CH2,CH]=[CH][$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"C1=[C,N][$(S(=O)(=O)),$(C=[N,O]),$(S=O)][C,N]=C1c2ccccc2",
+				"[CH2,CH]=C1C(=[O,SX2])**C1",
+				"c1c([OH,NH2,NH])c([OH,NH2,NH,$(N=N),$(N(C)C)])ccc1",
+				"c1c([OH,NH2,NH])ccc([OH,NH2,NH,$(N=N),$(N(C)C)])c1",
+				"c1([OH])c(O[CH3])cccc1",
+				"c1([OH])ccc(O[CH3])cc1",
+				"c1c([OH])ccc(C=C[CH3])c1",
+				"c1c([OH,NH2,NH])cc([OH,NH2,NH,$(N(C)C)])cc1",
+				"C([F,Cl,Br,I])[CH2,CH][$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"[$([CH]=[CH2,CH]),$(C(C)=[CH2,CH]),$(C#C);!$(C(C)=CC)][CH2][OH]",
+				"[CH2]=C[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"c1([OH])ccc([CH2][CH]=[CH2])cc1",
+				"c1(O[CH3])ccc([CH2][CH]=[CH2])cc1",
+				"[OH]c1cccc2ccccc12",
+				"F[CH2,CH]C(F)[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"Cl[CH2,CH]C(Cl)[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"Br[CH2,CH]C(Br)[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"I[CH2,CH]C(I)[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"aC=C[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"C#C[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"[CH2,CH]=[CH]C=C[$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"[CHR]=[CR][$(N(=O)~O),$(C=O),$(C#N),$(S=O),$(C(=O)N),$(a)]",
+				"C=C([F,Cl,Br,I])[F,Cl,Br,I]",
+				"c1c(=[O,NH2,NH])c(=[O,NH2,NH])ccc1",
+				"c1c(=[O,NH2,NH])ccc(=[O,NH2,NH])c1"
+			};
+			
+		}
+		@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[] {
+				"[!$(C=C);!$(C#C)]C(=[O,SX1,N])[F,Cl,Br,I]",
+				"[!$(C=C);!$(C#C)]C(=[O,SX1,N])[O,S,N][a]",
+				"[!$(C=C);!$(C#C)]C(=[O,SX1,N])[O,S,N]C(=[O,SX1,N])",
+				"[!$(C=C);!$(C#C)]C(=[O,S,N])[O,S][$(C=C),$(C=N),$(C#C),$(C#N)]",
+				"[#6]1C(=[O,S])[O,N,S][#6]1",
+				"[C,N,O,S,a]c1[n,o,s]c2ccccc2[n,o,s]1",
+				"[#6]1[#6](=[N,O,S])[#7,#8,#16][#6][#7,#8,#16]1",
+				"[C,O]=[#6]1[#7,#8,#16][#6](=[O,N,SX1])c2ccccc12",
+				"[!$(C=C);!$(C#C)]C(=[O,SX1,N])[O,S,N][CX4,O,S][$(C=O),a,$(C=C),$(C#C),$(C=N),$(C#N)]"
+			};
+		}
+		@Override
+		public String getExample(boolean value) {
+			return value?"Cc1oc2ccccc2n1":"C";
+		}
+		@Override
+		public String getShortName() {
+			return "acyl";
+		}
+	},
+	SN2 {
+		@Override
+		public String getCategoryExplanation() {
+			return "Structural Alert Identified for potential second order nucleophilic aliphatic substitution reaction.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "Alert for SN2 identified.";
+		}
+		@Override
+		public String getTitle() {
+			return "SN2-Nucleophilic Aliphatic Substitution";
+		}
+		@Override
+		public String getExplanation() {
+			return "to be a substrate for second-order nucleophilic substitution, or a precursor for it.";
+		}
+		@Override
+		public String[] getSMARTS() {
+			return new String[] {
+				"[CH,CH2,CH3;!$([CH2]CC=[O,S])][F,Cl,Br,I,$(OS(=O)(=O)[#6,#1]),$(OS(=O)(=O)O[#6,#1])]",
+				"[#6]1[O,N,SX2][#6]1",
+				"C1C(=[O,S])[O,S][CH2,CH]1",
+				"[$(C=C),$(C#C),a][CH2,CH][O,S][$([CH]=O),$([CH]=S),$(C(C)=O),$(C(C)=S),a]",
+				"[#6]1=,:[#6]C(=[O,SX1])N[SX2]1",
+				"[#6][O,SX2,N][O,SX2,N][$([CH]=O),$([CH]=S),$(C(C)=O),$(C(C)=S),a]",
+				"[CH2,CH3][NX3][NX2]=[O,S]",
+				"c1ccc2cc3ccccc3cc2c1",
+				"c1ccc2c(c1)ccc3ccccc23"
+			};
+		}
+		@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 for skin sensitisation reactivity domains have been identified.";
+		}
+		@Override
+		public String getCategoryTitle() {
+			return "No skin sensitisation reactivity domains 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();
+	
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/skinsensitisation/categories/SkinSensitisationCategory.java

@@ -0,0 +1,50 @@
+/*
+Copyright (C) 2005-2013
+
+Contact: www.ideaconsult.net
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU 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.skinsensitisation.categories;
+
+import toxTree.tree.DefaultCategory;
+
+/*
+ * Parent class for all skin sens categories
+ */
+public class SkinSensitisationCategory extends DefaultCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -4309054614893919949L;
+	public SkinSensitisationCategory(SkinSensitisationAlerts alert) {
+		super(alert.getCategoryTitle(),alert.ordinal()+1);
+        setExplanation(alert.getCategoryExplanation());
+	}
+	@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.ToxicCategory;
+	}
+	@Override
+	public CategoryType getNegativeCategoryType() {
+		return CategoryType.InconclusiveCategory;
+	}
+}