toxtree.tree.cramer3.rules

Class RuleSMARTSSubstructureHydrolysis

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.cramer3.rules.RuleSMARTSSubstructureHydrolysis

All Implemented Interfaces:

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

Direct Known Subclasses:

RuleLactone, RuleQ1, RuleQ29, RuleQ8

public abstract class RuleSMARTSSubstructureHydrolysis
extends RuleSMARTSSubstructureAmbit
implements IRuleSMARTS

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected Reactor	reactor

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
RuleSMARTSSubstructureHydrolysis()

Method Summary

Modifier and Type	Method and Description
protected boolean	extraTest(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) Allows to apply non-SMART based tests
String	getImplementationDetails()
Reactor	getReactor()
protected abstract String[][]	getSmirks()
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

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

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

Methods inherited from interface toxtree.tree.cramer3.rules.IRuleSMARTS

getSMARTS

Field Detail

reactor

protected final transient Reactor reactor

Constructor Detail

RuleSMARTSSubstructureHydrolysis

public RuleSMARTSSubstructureHydrolysis()
                                 throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

getReactor

public Reactor getReactor()

getSmirks

protected abstract String[][] getSmirks()

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

extraTest

protected boolean extraTest(org.openscience.cdk.interfaces.IAtomContainer mol,
                            org.openscience.cdk.interfaces.IAtomContainer selected)
                     throws DecisionMethodException

Allows to apply non-SMART based tests

Parameters:

mol -

selected -

Returns:

Throws:

DecisionMethodException

verifyRule

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

Overrides:

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

Throws:

DecisionMethodException

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

Overrides:

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