toxtree.plugins.verhaar2

Class VerhaarScheme2

java.lang.Object

java.util.Observable

toxTree.tree.AbstractTree

toxTree.tree.UserDefinedTree

verhaar.VerhaarScheme

toxtree.plugins.verhaar2.VerhaarScheme2

All Implemented Interfaces:

ambit2.core.data.IObject2Properties<UserDefinedTree>, ambit2.core.data.IStructureDiagramDepiction<BufferedImage>, ambit2.core.data.IStructureDiagramHighlights, Serializable, Cloneable, Observer, net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor, IDecisionInteractive, IDecisionMethod, IDecisionMethodPrority, XMLSerializable

public class VerhaarScheme2
extends VerhaarScheme

An implementaton of Verhaar scheme for predicting toxicity mode of action.

• Verhaar HJM, van Leeuwen CJ and Hermens JLM (1992) Classifying environmental pollutants. 1. Structure-activity relationships for prediction of aquatic toxicity. Chemosphere 25, 471-491.
• Verhaar HJM, Mulder W and Hermens JLM (1995) QSARs for ecotoxicity. In: Overview of structure-activity relationships for environmental endpoints, Part 1: General outline and procedure. Hermens JLM (Ed), Report prepared within the framework of the project "QSAR for Prediction of Fate and Effects of Chemicals in the Environment", an international project of the Environment; Technologies RTD Programme (DGXII/D-1) of the Europenan Commission under contract number EV5V-CT92-0211.
• Verhaar HJM, Solbe J, Speksnijder J, van Leeuwen CJ and Hermens JLM (2000) Classifying environmental pollutants: Part 3. External validation of the classification system. Chemosphere 40, 875-883.

Updated according to recommendation in

• S.J. Enoch, M. Hewitt, M.T.D. Cronin, S. Azam, J.C. Madden, Classification of chemicals according to mechanism of aquatic toxicity: An evaluation of the implementation of the Verhaar scheme in Toxtree, Chemosphere 73 (2008) 243-248

Rules:

• LogP limits
• structural rules
• implementation in verhaar.rules package

Categories:

• implementation in verhaar.categories package

Author:

Nina Jeliazkova Modified 2005-8-14

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface toxTree.core.IDecisionInteractive

IDecisionInteractive.UserOptions

Field Summary

Fields inherited from class verhaar.VerhaarScheme

c_categories, c_rules_normal, c_rules_reversed

Fields inherited from class toxTree.tree.UserDefinedTree

editable, listener, nodesFactory, options

Fields inherited from class toxTree.tree.AbstractTree

categories, changes, explanation, falseIfRuleNotImplemented, imageSize, logger, modified, name, priority, rules, treeRoot, web

Fields inherited from interface toxTree.core.XMLSerializable

xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT

Constructor Summary

Constructors

Constructor and Description
VerhaarScheme2()
VerhaarScheme2(boolean reversed)

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()

Methods inherited from class toxTree.tree.UserDefinedTree

calculate, clone, close, createArrayResult, getBranch, getBranch, getCategory, getCategory, getDescriptorNames, getDescriptorResultType, getID, getInteractive, getListener, getNodesFactory, getOptions, getParameterNames, getParameters, getParameterType, getRule, hasUnreachableRules, hasUnusedCategories, initialise, initRules, isEditable, isEnabled, open, process, removeListener, setArrayValue, setEditable, setEnabled, setInteractive, setListener, setNodesFactory, setOptions, setParameters, setParameters, setTransitions, toString, verifyRules, visitCategories, visitRules

Methods inherited from class toxTree.tree.AbstractTree

addDecisionRule, addPropertyChangeListener, classify, clearChanged, createDecisionResult, equals, explainRules, fromXML, getCategories, getEditor, getExplanation, getImage, getImage, getImageSize, getLegend, getNumberOfClasses, getNumberOfRules, getPriority, getRule, getRules, getTitle, getTopRule, isFalseIfRuleNotImplemented, isModified, isWeb, optionsPanel, printResults, printToStream, removePropertyChangeListener, retrieveExplanation, setCategories, setChanged, setDecisionRule, setExplanation, setFalseIfRuleNotImplemented, setImageSize, setModified, setPriority, setRules, setRules, setTitle, setWeb, testRulesWithSelector, toShallowXML, toXML, update, verifyResidues, verifyRules, walkRules, walkRules

Methods inherited from class java.util.Observable

addObserver, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VerhaarScheme2

public VerhaarScheme2()
               throws DecisionMethodException

Throws:

DecisionMethodException

VerhaarScheme2

public VerhaarScheme2(boolean reversed)
               throws DecisionMethodException

Throws:

DecisionMethodException

Method Detail

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

Overrides:

getSpecification in class VerhaarScheme