toxTree.tree.rules.smarts
Class RuleSMARTSSubstructureAmbit

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
              extended by toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.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, RuleAlertsNarcosis1_1_2_1, RuleAlertsNarcosis1_1_2_3, RuleAlkylAldehyde, RuleAlkylHydrazine, RuleAlkylPhosphonate, RuleAmine, RuleAromatic, RuleAromaticAldehyde, 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, 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
RuleSMARTSSubstructureAmbit()
           
 
Method Summary
 ambit2.smarts.query.ISmartsPattern createSmartsPattern(java.lang.String smarts, boolean negate)
           
protected  org.openscience.cdk.interfaces.IAtomContainer getObjectToVerify(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(java.lang.String smarts,
                                                              boolean negate)
                                                       throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException


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