toxTree.tree.rules.smarts

Class RuleSMARTSubstructureCDK

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

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

toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK

All Implemented Interfaces:

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

Direct Known Subclasses:

QSAR6Applicable, QSAR6Applicable, Rule14Aliphatic_glycerol_monoethers, Rule15, Rule16, Rule17, Rule18, Rule19, Rule20, Rule21, Rule23, Rule24, Rule25, Rule26, Rule27, Rule28, Rule29, Rule31, Rule32, Rule34, Rule35, Rule36, Rule37, RuleABUnsaturatedAldehyde, RuleABUnsaturatedAldehyde, RuleAromaticDiazo, RuleAromaticDiazo, RuleDerivedAromaticAmines, RuleDerivedAromaticAmines, RulePhenols, StructureAlertCDK

public class RuleSMARTSubstructureCDK
extends AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>

An IDecisionRule, making use of CDK SMARTS parser.

Author:

Nina Jeliazkova nina@acad.bg

See Also:

Serialized Form

Field Summary

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
RuleSMARTSubstructureCDK()

Method Summary

Modifier and Type	Method and Description
ambit2.smarts.query.ISmartsPattern	createSmartsPattern(String smarts, boolean negate)
protected org.openscience.cdk.interfaces.IAtomContainer	getObjectToVerify(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.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

Constructor Detail

RuleSMARTSubstructureCDK

public RuleSMARTSubstructureCDK()

Method Detail

createSmartsPattern

public ambit2.smarts.query.ISmartsPattern createSmartsPattern(String smarts,
                                                              boolean negate)
                                                       throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

getObjectToVerify

protected org.openscience.cdk.interfaces.IAtomContainer getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

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

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