toxtree.plugins.ames.rules

Class SA10_gen

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

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

toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK

toxTree.tree.rules.StructureAlertCDK

toxtree.plugins.ames.rules.SA10_gen

All Implemented Interfaces:

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

public class SA10_gen
extends StructureAlertCDK

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	AB_UNSATURATED_CARBONYLS
protected static String	AB_UNSATURATED_CARBONYLS_SMARTS
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	query

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
SA10_gen()

Method Summary

Modifier and Type	Method and Description
boolean	CH6SubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)
org.openscience.cdk.interfaces.IAtomContainerSet	detachSubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class toxTree.tree.rules.StructureAlertCDK

getImplementationDetails, incrementCounter

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

Field Detail

AB_UNSATURATED_CARBONYLS

protected static String AB_UNSATURATED_CARBONYLS

AB_UNSATURATED_CARBONYLS_SMARTS

protected static String AB_UNSATURATED_CARBONYLS_SMARTS

query

protected transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer query

Constructor Detail

SA10_gen

public SA10_gen()
         throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

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 StructureAlertCDK

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

detachSubstituentAtBetaCarbon

public org.openscience.cdk.interfaces.IAtomContainerSet detachSubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)

CH6SubstituentAtBetaCarbon

public boolean CH6SubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)