toxtree.tree.cramer3.rules

Class RuleQ9_D

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

toxtree.tree.cramer3.rules.RuleLactone

toxtree.tree.cramer3.rules.RuleQ9_D

All Implemented Interfaces:

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

public class RuleQ9_D
extends RuleLactone

See Also:

Serialized Form

Field Summary

Fields inherited from class toxtree.tree.cramer3.rules.RuleLactone

tag, tag_ring

Fields inherited from class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis

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
RuleQ9_D()

Method Summary

Modifier and Type	Method and Description
protected boolean	allowedRingsOfAtom(org.openscience.cdk.interfaces.IRingSet allrings, org.openscience.cdk.interfaces.IAtom atom) returns false if the ring is conjugated (all C atoms are C.sp2)
protected boolean	extraTest(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) Allows to apply non-SMART based tests
protected String[][]	getSmirks()

Methods inherited from class toxtree.tree.cramer3.rules.RuleLactone

getSMARTS, isFused, tagRings, verifyRule

Methods inherited from class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis

getImplementationDetails, getReactor, verifyRule

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

Constructor Detail

RuleQ9_D

public RuleQ9_D()
         throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

getSmirks

protected String[][] getSmirks()

Specified by:

getSmirks in class RuleSMARTSSubstructureHydrolysis

extraTest

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

Description copied from class: RuleSMARTSSubstructureHydrolysis

Allows to apply non-SMART based tests

Overrides:

extraTest in class RuleSMARTSSubstructureHydrolysis

Returns:

Throws:

DecisionMethodException

allowedRingsOfAtom

protected boolean allowedRingsOfAtom(org.openscience.cdk.interfaces.IRingSet allrings,
                                     org.openscience.cdk.interfaces.IAtom atom)

returns false if the ring is conjugated (all C atoms are C.sp2)

Overrides:

allowedRingsOfAtom in class RuleLactone