toxTree.tree.rules.smarts
Class RuleSMARTSubstructureCDK

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.RuleSMARTSubstructureCDK
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures
Direct Known Subclasses:
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, RuleAromaticDiazo, 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
RuleSMARTSubstructureCDK()
           
 
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)
           
 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(java.lang.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


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