toxTree.tree.rules.smarts

Class RuleSMARTSSubstructureAmbit

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

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

toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit

All Implemented Interfaces:

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

Direct Known Subclasses:

KroesRule3, Rule151, Rule152, Rule153, Rule154, Rule171, Rule24, Rule31, Rule32, Rule33, Rule33, Rule34, Rule35, Rule36, Rule37, Rule38, Rule39, RuleAlcohol, RuleAldehyde, RuleAlertsNarcosis1_1_1, RuleAlertsNarcosis1_1_1_1, RuleAlertsNarcosis1_1_2_1, RuleAlertsNarcosis1_1_2_3, RuleAlkylAldehyde, RuleAlkylHydrazine, RuleAlkylPhosphonate, RuleAmine, RuleAromatic, RuleAromaticAldehyde, RuleAromaticAmineNoSulfonicGroup, RuleAromaticAmineNoSulfonicGroup, RuleAromaticAzo, RuleAromaticNitro, RuleArylMethylHalide, RuleAziridine, RuleAzo, RuleBenzene, RuleEpoxide, RuleEther, RuleFreeABUnsaturatedHetero, RuleFuran, RuleHalide, RuleHeteroaromatic, RuleHeterocycle, RuleHydrazine, RuleIminomethyl, RuleKetone, RuleNChloramine, RuleNHydroxy, RuleNitro, RuleNitrogenMustard, RuleNitrosamine, RuleNitroso, RuleNMethylol, RuleNOxide, RuleNucleosides, RulePhosphoricGroups, RuleprimaryAlkylHalide, RulePropiolactone, RuleQ10, RuleQ13, RuleQ15, RuleQ17, RuleQ19, RuleQ2, RuleQ20, RuleQ21, RuleQ22, RuleQ27, RuleQ28, RuleQ3, RuleQ4A, RuleQ5, RuleQ9_A, RuleQ9_B, RuleRingsSMARTSSubstituents, RuleSMARTSSubstructureHydrolysis, RuleSMARTSSubstructureTagged, RuleSMARTSubstructure, RuleUnchargedOrganophosphates, RuleUrethaneDerivatives, StructureAlert, StructureAlertAmbit

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

An IDecisionRule, making use of Ambit SMARTS parser. http://ambit.sourceforge.net/AMBIT2-LIBS/ambit2-smarts/index.html http://onlinelibrary.wiley.com/doi/10.1002/minf.201100028/abstract

Author:

Nina Jeliazkova jeliazkova.nina@gmail.com

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
RuleSMARTSSubstructureAmbit()

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)
protected org.openscience.cdk.interfaces.IRingSet	hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)

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, 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

RuleSMARTSSubstructureAmbit

public RuleSMARTSSubstructureAmbit()

Method Detail

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>

createSmartsPattern

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

Throws:

ambit2.smarts.query.SMARTSException

hasRingsToProcess

protected org.openscience.cdk.interfaces.IRingSet hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws DecisionMethodException

Throws:

DecisionMethodException