toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/categories/DNABindingCategory.java

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+/*
+Copyright Ideaconsult Ltd (C) 2005-2013 
+Contact: Ideaconsult Ltd.
+
+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 toxtree.plugins.dnabinding.categories;
+
+import toxTree.tree.DefaultCategory;
+
+/*
+ * Parent class for all skin sens categories
+ */
+public abstract class DNABindingCategory extends DefaultCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -4309054614893919949L;
+	public DNABindingCategory(DNABindingAlerts alert) {
+		super(alert.getCategoryTitle(),alert.ordinal()+1);
+        setExplanation(alert.getCategoryExplanation());
+	}
+	
+	@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.ToxicCategory;
+	}
+	@Override
+	public CategoryType getNegativeCategoryType() {
+		return CategoryType.InconclusiveCategory;
+	}
+}

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

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+/*
+Copyright (C) 2005-2013
+
+Contact: Ideaconsult Ltd.
+
+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.dnabinding.categories;
+
+
+
+/**
+ * Michael Acceptors
+ * @author nina
+ *
+ */
+public class MichaelAcceptors extends DNABindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4861205974087430140L;
+	public MichaelAcceptors() {
+		super(DNABindingAlerts.MICHAEL_ACCEPTORS);
+	}
+
+}

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

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+/*
+Copyright (C) 2005-2013
+
+Contact: Ideaconsult Ltd.
+
+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.dnabinding.categories;
+
+/**
+ * No alerts
+ * @author nina
+ *
+ */
+public class NoAlerts extends DNABindingCategory {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6055850368701920221L;
+	public NoAlerts() {
+		super(DNABindingAlerts.NO_ALERTS);
+	}
+	
+	@Override
+	public CategoryType getCategoryType() {
+		return CategoryType.NontoxicCategory;
+	}
+	@Override
+	public CategoryType getNegativeCategoryType() {
+		return CategoryType.ToxicCategory;
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/dnabinding/categories/SN1Alerts.java

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+/*
+Copyright (C) 2005-2013
+
+Contact: Ideaconsult Ltd.
+
+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.dnabinding.categories;
+
+
+
+/**
+ * Substrate has structural alerts for Nucleophilic Aromatic Substitution
+ * @author nina
+ *
+ */
+public class SN1Alerts extends DNABindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5734136598332428372L;
+
+	public SN1Alerts() {
+		super(DNABindingAlerts.SN1);
+	}
+
+}

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

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+/*
+Copyright (C) 2005-2013
+
+Contact: Ideaconsult Ltd.
+
+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.dnabinding.categories;
+
+
+
+/**
+ * second order nucleophilic aliphatic substitution reaction
+ * @author nina
+ *
+ */
+public class SN2Alerts extends DNABindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -3176004732905640400L;
+
+	public SN2Alerts() {
+		super(DNABindingAlerts.SN2);
+	}
+	
+}

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

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+/*
+Copyright (C) 2005-2013
+
+Contact: Ideaconsult Ltd.
+
+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.dnabinding.categories;
+
+
+
+/**
+ * Shiff base
+ * @author nina
+ *
+ */
+public class ShiffBaseAlerts extends DNABindingCategory {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 6055850368701920221L;
+	public ShiffBaseAlerts() {
+		super(DNABindingAlerts.SHIFF_BASE);
+	}
+
+}

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

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+package toxtree.plugins.dnabinding.rules;
+
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+
+
+
+/**
+ * Acyl transfer
+ * @author nina
+ *
+ */
+public class AcylTransferRule extends DNABindingRule {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -1916992749211312250L;
+
+	public AcylTransferRule() {
+		super(DNABindingAlerts.ACYL_TRANSFER);
+	}
+}

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

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+package toxtree.plugins.dnabinding.rules;
+
+import java.util.logging.Level;
+
+import toxTree.tree.rules.StructureAlert;
+import toxtree.plugins.dnabinding.categories.DNABindingAlerts;
+import ambit2.smarts.query.SMARTSException;
+
+/**
+ *  Parent class for all skin sens rules
+ * @author nina
+ *
+ */
+public class DNABindingRule extends StructureAlert {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -1658487497286276204L;
+	protected String shortName;
+	public DNABindingRule(DNABindingAlerts alert) {
+		super();
+		try {
+			
+			//setID(Integer.toString(alert.ordinal()+1));
+			setID(alert.getShortName());
+			setTitle(alert.getTitle());
+			setExplanation(alert.getExplanation());
+			setContainsAllSubstructures(false);
+			String[][] smarts = alert.getSMARTS();
+			for (int i=0; i < smarts.length;i++)
+				//title, smars
+				addSubstructure(String.format("%s > %s",smarts[i][0],smarts[i][1]),smarts[i][2]);
+			
+			examples[0] = alert.getExample(false);
+			examples[1] = alert.getExample(true);	
+	
+		} catch (SMARTSException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+		}
+	}	
+
+}

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

@@ -0,0 +1,225 @@
+/*
+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.dnabinding.rules;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.logging.Level;
+
+import net.idea.modbcum.i.exceptions.AmbitException;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+import toxTree.core.IDecisionCategories;
+import toxTree.core.IDecisionCategory;
+import toxTree.core.IDecisionRule;
+import toxTree.data.CategoryFilter;
+import toxTree.exceptions.DMethodNotAssigned;
+import toxTree.exceptions.DecisionResultException;
+import toxTree.tree.DecisionNode;
+import toxTree.tree.ProgressStatus;
+import toxTree.tree.RuleResult;
+import toxTree.tree.TreeResult;
+import toxTree.tree.rules.IAlertCounter;
+import ambit2.base.data.ILiteratureEntry;
+import ambit2.base.data.ILiteratureEntry._type;
+import ambit2.base.data.Property;
+import ambit2.base.data.PropertyAnnotation;
+import ambit2.base.data.PropertyAnnotations;
+
+public class DNABindingTreeResult extends TreeResult {
+    protected static String SUFFIX = "SUFFIX";
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -1505391697761215610L;
+
+	
+	public void assignResult(IAtomContainer mol) throws DecisionResultException {
+		if (mol == null) return;
+		IDecisionCategories c = decisionMethod.getCategories();
+		for (int i=0; i < c.size();i++) {
+			String result = Answers.toString(Answers.NO);
+			if (getAssignedCategories().indexOf(c.get(i))>-1)
+				result = Answers.toString(Answers.YES);
+			mol.setProperty(
+	        		c.get(i).toString(),
+	                result);
+		}
+		/*
+        String paths = getClass().getName()+"#explanation";
+        if (getDecisionMethod().getRules().size() > 1) {
+	        mol.setProperty(
+	        		paths,
+	                explain(false).toString());
+	        Hashtable<String,String> b = getExplanation(mol);
+	        Enumeration<String> k = b.keys();
+	        while (k.hasMoreElements()) {
+	        	String key = k.nextElement();
+	        	mol.setProperty(key,b.get(key));
+	        }
+        } else
+        	mol.removeProperty(paths);
+        	*/
+        firePropertyChangeEvent(ProgressStatus._pRuleResult, null, status);        
+	}
+	
+	@Override
+	public List<Property> getResultProperties() throws AmbitException {
+
+		if (getDecisionMethod() == null) throw new AmbitException("Unassigned method");
+		ILiteratureEntry le = getReference();
+		le.setType(_type.Algorithm);
+		List<Property> p = new ArrayList<Property>();
+		for (IDecisionCategory category : getDecisionMethod().getCategories()) {
+			Property property = new Property(category.toString(),le);
+			property.setLabel(le.getURL());
+			property.setClazz(String.class);
+			property.setOrder(p.size()+1);
+			property.setEnabled(true);
+			property.setNominal(true);
+			PropertyAnnotations pa = new PropertyAnnotations();
+			property.setAnnotations(pa);
+			PropertyAnnotation a = new PropertyAnnotation();
+			a.setType("^^"+category.getCategoryType().name());
+			a.setPredicate("acceptValue");
+			a.setObject(Answers.toString(Answers.YES));
+			pa.add(a);
+			a = new PropertyAnnotation();
+			a.setType("^^"+category.getNegativeCategoryType().name());
+			a.setPredicate("acceptValue");
+			a.setObject(Answers.toString(Answers.NO));
+			pa.add(a);
+			p.add(property);
+		}
+		
+		Property property = new Property(String.format("%s#explanation", getDecisionMethod().getTitle()),le); 
+		property.setLabel(le.getURL());
+		property.setClazz(String.class);
+		property.setOrder(p.size()+1);
+		property.setEnabled(true);
+		property.setNominal(false);
+		p.add(property);
+		
+		return p;
+	}
+	
+	public void addRuleResult(IDecisionRule rule, boolean value, IAtomContainer molecule)
+	throws DecisionResultException {
+			super.addRuleResult(rule, value,molecule);
+			if (rule instanceof RuleDNABindingAlerts)
+				setSilent(true);
+
+			else setSilent((rule instanceof DecisionNode) &&	
+					(
+				(((DecisionNode)rule).getRule() instanceof RuleDNABindingAlerts) 
+
+
+				)
+				);
+				
+					
+	}
+
+	@Override
+	public String[] getResultPropertyNames() {
+		IDecisionCategories c = decisionMethod.getCategories();
+		String[] names = new String[c.size()];
+		for (int i=0; i < c.size();i++) 
+			names[i] = c.get(i).toString();
+		return names;
+	}
+	
+	public Hashtable<String,String> getExplanation(IAtomContainer mol) throws DecisionResultException {
+		Hashtable<String,String> b = new  Hashtable<String,String>();
+
+        IAtomContainer originalMol = getOriginalMolecule();
+		try {
+		    if (status.isEstimated()) {
+		    	for (int i=0;i < ruleResults.size();i++) {
+		    		RuleResult r = ((RuleResult)ruleResults.get(i));
+		    		if (r.isSilent()) continue;
+
+		    		if ((r.getCategory() == null) 
+		    			|| (r.getRule() instanceof IAlertCounter)
+		    			|| (
+		    			(r.getRule() instanceof DecisionNode) && (((DecisionNode)r.getRule()).getRule() instanceof IAlertCounter)
+		    			)
+		    			) { //not a leaf node or an alert
+		    			if (r.isResult())
+		    				b.put(r.getRule().getID(),Answers.toString(Answers.YES));
+		    			else 
+		    				b.put(r.getRule().getID(),Answers.toString(Answers.NO));
+		    		}
+		    		//Use this to get descriptor values 
+
+		    	}
+		    	
+		    } else if (status.isEstimating()) {
+		        b.put(ProgressStatus._eResultIsEstimating,"YES");
+		        
+		    }   else if (status.isError()) {
+		        b.put(ProgressStatus._eError,status.getErrMessage());
+		    }
+
+		//} catch (DecisionMethodException x) {
+			//throw new DecisionResultException(x);
+		} catch (NullPointerException x) {
+			throw new DMethodNotAssigned(ProgressStatus._eMethodNotAssigned);
+		}
+		return b;
+	}
+	
+    public List<CategoryFilter> getFilters() {
+
+    	ArrayList<CategoryFilter> l = new ArrayList<CategoryFilter>();
+    	IDecisionCategories c = getDecisionMethod().getCategories();
+		for (int i=0; i < c.size();i++) 
+		try { 
+    		l.add(new CategoryFilter(c.get(i).toString(),Answers.toString(Answers.YES)));
+    		l.add(new CategoryFilter(c.get(i).toString(),Answers.toString(Answers.NO)));
+    	} catch (Exception x) {
+    		logger.log(Level.SEVERE,x.getMessage(),x);
+    	}
+    	return l;
+    }
+}
+
+class Answers {
+	public static int NO=0;
+	public static int YES=1;
+	protected Answers() {
+		
+	}
+	public static String toString(int answer) {
+		switch (answer) {
+		case 0: return "NO";
+		case 1: return "YES";
+		default: return "";
+		}
+	}
+}