toxtree.plugins.ames.rules

Class RuleDerivedAromaticAmines

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.plugins.ames.rules.RuleDerivedAromaticAmines

All Implemented Interfaces:

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

public class RuleDerivedAromaticAmines
extends RuleSMARTSubstructureCDK

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer[]	groups

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
RuleDerivedAromaticAmines()

Method Summary

Modifier and Type	Method and Description
protected void	deriveAmine(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, org.openscience.cdk.interfaces.IAtomContainerSet origin, org.openscience.cdk.interfaces.IAtomContainerSet results)
org.openscience.cdk.interfaces.IAtomContainerSet	detachSubstituent(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, org.openscience.cdk.interfaces.IAtomContainer c)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	group1()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	group2()
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, getImplementationDetails, 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

groups

protected transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer[] groups

Constructor Detail

RuleDerivedAromaticAmines

public RuleDerivedAromaticAmines()

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 RuleSMARTSubstructureCDK

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

deriveAmine

protected void deriveAmine(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                           org.openscience.cdk.interfaces.IAtomContainerSet origin,
                           org.openscience.cdk.interfaces.IAtomContainerSet results)

group1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group1()

group2

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group2()

detachSubstituent

public org.openscience.cdk.interfaces.IAtomContainerSet detachSubstituent(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                                                                          org.openscience.cdk.interfaces.IAtomContainer c)