toxTree.tree.rules
Class StructureAlertCDK

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 toxTree.tree.rules.StructureAlertCDK
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IAlertCounter, IRuleSMARTSubstructures
Direct Known Subclasses:
FG1, SA1, SA1_gen, SA10, SA10_gen, SA11, SA11_gen, SA13, SA13_gen, SA17_nogen, SA2, SA2_gen, SA22, SA22_gen, SA23, SA23_gen, SA24, SA24_gen, SA25, SA25_gen, SA27, SA27_gen, SA28, SA28bis, SA28bis_gen, SA28ter, SA28ter_gen, SA29, SA29_gen, SA31a_nogen, SA37_gen, SA38_gen, SA39_gen_and_nogen, SA4, SA4_gen, SA40_nogen, SA41_nogen, SA42_nogen, SA43_nogen, SA44_nogen, SA45_nogen, SA46_nogen, SA47_nogen, SA48_nogen, SA49_nogen, SA50_nogen, SA51_nogen, SA52_nogen, SA53_nogen, SA54_nogen, SA55_nogen, SA56_nogen

public class StructureAlertCDK
extends RuleSMARTSubstructureCDK
implements IAlertCounter

See Also:
Serialized Form

Field Summary
 
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
StructureAlertCDK()
           
 
Method Summary
 java.lang.String getImplementationDetails()
           
 void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 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, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, isAPossibleHit, 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
 

Constructor Detail

StructureAlertCDK

public StructureAlertCDK()
Method Detail

incrementCounter

public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
Specified by:
incrementCounter in interface IAlertCounter

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

getImplementationDetails

public java.lang.String getImplementationDetails()
Specified by:
getImplementationDetails in interface IImplementationDetails
Overrides:
getImplementationDetails in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>


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