toxTree.qsar

Class LinearDiscriminantRule

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.qsar.LinearDiscriminantRule

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IDescriptorBased, IImplementationDetails, XMLSerializable

Direct Known Subclasses:

RuleDACancerogenicityAromaticAmines, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityAromaticAmines, RuleDAMutagenicityAromaticAmines

public abstract class LinearDiscriminantRule
extends AbstractRule
implements IImplementationDetails, IDescriptorBased

Uses LinearQSARModel and returns true if LinearQSARModel.predict(IAtomContainer) is >= getThreshold() and false otherwise.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static Hashtable<String,String>	dictionary
protected LinearQSARModel	model
protected double	threshold

Fields inherited from class toxTree.tree.AbstractRule

changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title

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
LinearDiscriminantRule()
LinearDiscriminantRule(LinearQSARModel model, double threshold)

Method Summary

Modifier and Type	Method and Description
protected boolean	compare(double value, double threshold)
protected abstract DRuleException	createException(ambit2.base.exceptions.QSARModelException x)
String	getImplementationDetails()
LinearQSARModel	getModel()
ambit2.rendering.IAtomContainerHighlights	getSelector()
double	getThreshold()
protected String	hint()
boolean	isCalculated(String name)
boolean	isImplemented()
void	setCalculated(org.openscience.cdk.qsar.IMolecularDescriptor descriptor, String name, boolean calculated)
void	setModel(LinearQSARModel model)
void	setThreshold(double threshold)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, equals, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

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

Field Detail

dictionary

protected static Hashtable<String,String> dictionary

model

protected LinearQSARModel model

threshold

protected double threshold

Constructor Detail

LinearDiscriminantRule

public LinearDiscriminantRule(LinearQSARModel model,
                              double threshold)

LinearDiscriminantRule

public LinearDiscriminantRule()

Method Detail

getThreshold

public double getThreshold()

setThreshold

public void setThreshold(double threshold)

getModel

public LinearQSARModel getModel()

setModel

public void setModel(LinearQSARModel model)

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException

Description copied from interface: IDecisionRule

This is the core of a IDecisionRule behaviour. The method returns true if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer and FALSE if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer??

Specified by:

verifyRule in interface IDecisionRule

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

createException

protected abstract DRuleException createException(ambit2.base.exceptions.QSARModelException x)

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class AbstractRule

Returns:

false if the rule is not implemented and true if it is

compare

protected boolean compare(double value,
                          double threshold)

hint

protected String hint()

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

isCalculated

public boolean isCalculated(String name)

Specified by:

isCalculated in interface IDescriptorBased

setCalculated

public void setCalculated(org.openscience.cdk.qsar.IMolecularDescriptor descriptor,
                          String name,
                          boolean calculated)

Specified by:

setCalculated in interface IDescriptorBased

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule