mutant.rules
Class QSAR6Applicable

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
              extended by toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
                  extended by mutant.rules.QSAR6Applicable
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.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
protected static java.lang.String aromatic_amine
           
protected  java.beans.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
QSAR6Applicable()
           
 
Method Summary
 boolean getInteractive()
           
 java.beans.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(java.beans.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 java.lang.String aromatic_amine

options

protected IDecisionInteractive.UserOptions options

listener

protected java.beans.PropertyChangeListener listener
Constructor Detail

QSAR6Applicable

public QSAR6Applicable()
                throws java.lang.Exception
Throws:
java.lang.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 java.beans.PropertyChangeListener getListener()
Specified by:
getListener in interface IDecisionInteractive

setListener

public void setListener(java.beans.PropertyChangeListener listener)
Specified by:
setListener in interface IDecisionInteractive

removeListener

public void removeListener()
Specified by:
removeListener in interface IDecisionInteractive


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