toxTree.tree.rules

Class StructureAlertAmbit

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

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

toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit

toxTree.tree.rules.StructureAlertAmbit

All Implemented Interfaces:

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

Direct Known Subclasses:

Rule1, Rule10A, Rule10B, Rule11, Rule12A, Rule12B, Rule13A, Rule13B, Rule14, Rule2, Rule3, Rule4A, Rule4B, Rule5, Rule6, Rule7, Rule8, Rule9A, Rule9B, SA26_gen, SA26_gen, SA28_gen, SA28_gen

public class StructureAlertAmbit
extends RuleSMARTSSubstructureAmbit
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

Constructors

Constructor and Description
StructureAlertAmbit()

Method Summary

Modifier and Type	Method and Description
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.RuleSMARTSSubstructureAmbit

createSmartsPattern, getObjectToVerify, hasRingsToProcess

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

StructureAlertAmbit

public StructureAlertAmbit()

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 AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

Overrides:

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