toxtree.plugins.ames.rules

Class QSAR6Applicable

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>

toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK

toxtree.plugins.ames.rules.QSAR6Applicable

All Implemented Interfaces:

ambit2.smarts.query.ISmartsPatternFactory, Serializable, Cloneable, IDecisionInteractive, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures

public class QSAR6Applicable
extends RuleSMARTSubstructureCDK
implements IDecisionInteractive

See Also:

Serialized Form

Nested Class Summary

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

IDecisionInteractive.UserOptions

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	aromatic_amine
protected PropertyChangeListener	listener
protected IDecisionInteractive.UserOptions	options

Fields inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure

containsAllSubstructures, final_and_patch, smartsPatterns

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
QSAR6Applicable()

Method Summary

Modifier and Type	Method and Description
boolean	getInteractive()
PropertyChangeListener	getListener()
IDecisionInteractive.UserOptions	getOptions()
protected boolean	isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) Returns true always.
boolean	isSkipRule()
void	removeListener()
void	setInteractive(boolean value)
void	setListener(PropertyChangeListener listener)
void	setOptions(IDecisionInteractive.UserOptions options)
void	setSkipRule(boolean value)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK

createSmartsPattern, getObjectToVerify

Methods inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure

addSubstructure, addSubstructure, addSubstructure, clearSubstructures, containsAllSubstructures, deleteSubstructure, equals, getImplementationDetails, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, isImplemented, removeSingleSMARTS, setContainsAllSubstructures, setSmartsPatterns, setSubstructure, setSubstructure, verifyRule

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, 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

aromatic_amine

protected static String aromatic_amine

options

protected IDecisionInteractive.UserOptions options

listener

protected PropertyChangeListener listener

Constructor Detail

QSAR6Applicable

public QSAR6Applicable()
                throws Exception

Throws:

Exception

Method Detail

getOptions

public IDecisionInteractive.UserOptions getOptions()

Specified by:

getOptions in interface IDecisionInteractive

setOptions

public void setOptions(IDecisionInteractive.UserOptions options)

Specified by:

setOptions in interface IDecisionInteractive

isAPossibleHit

protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
                                 org.openscience.cdk.interfaces.IAtomContainer processedObject)
                          throws DecisionMethodException

Description copied from class: AbstractRuleSmartSubstructure

Returns true always. Override to apply simple prescreening for the rule;

Overrides:

isAPossibleHit in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>

Returns:

Throws:

DecisionMethodException

setInteractive

public void setInteractive(boolean value)

Specified by:

setInteractive in interface IDecisionInteractive

setSkipRule

public void setSkipRule(boolean value)

isSkipRule

public boolean isSkipRule()

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

Overrides:

verifyRule in class RuleSMARTSubstructureCDK

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

getInteractive

public boolean getInteractive()

Specified by:

getInteractive in interface IDecisionInteractive

getListener

public PropertyChangeListener getListener()

Specified by:

getListener in interface IDecisionInteractive

setListener

public void setListener(PropertyChangeListener listener)

Specified by:

setListener in interface IDecisionInteractive

removeListener

public void removeListener()

Specified by:

removeListener in interface IDecisionInteractive