toxtree.tree.cramer3.rules

Class RuleQ5

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.RuleQ5

All Implemented Interfaces:

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

public class RuleQ5
extends RuleSMARTSSubstructureAmbit
implements IRuleSMARTS

Derived from Q4 RuleHasOnlySaltSulphonateSulphate with additions and changes

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ambit2.smarts.processors.SMIRKSProcessor	neutraliser

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
RuleQ5()

Method Summary

Modifier and Type	Method and Description
String[][]	getSMARTS()
org.openscience.cdk.interfaces.IAtomContainer	neutralise(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, 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

neutraliser

protected ambit2.smarts.processors.SMIRKSProcessor neutraliser

Constructor Detail

RuleQ5

public RuleQ5()
       throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

neutralise

public org.openscience.cdk.interfaces.IAtomContainer neutralise(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                         throws Exception

Throws:

Exception

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

getSMARTS

public String[][] getSMARTS()

Specified by:

getSMARTS in interface IRuleSMARTS