mutant.rules
Class RuleDerivedAromaticAmines

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
                  extended by mutant.rules.RuleDerivedAromaticAmines
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures

public class RuleDerivedAromaticAmines
extends RuleSMARTSubstructureCDK

See Also:
Serialized Form

Field Summary
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer[] groups
           
 
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
RuleDerivedAromaticAmines()
           
 
Method Summary
protected  void deriveAmine(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, org.openscience.cdk.interfaces.IMoleculeSet origin, org.openscience.cdk.interfaces.IMoleculeSet results)
           
 org.openscience.cdk.interfaces.IMoleculeSet detachSubstituent(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, org.openscience.cdk.interfaces.IAtomContainer c)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group1()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group2()
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          This is the core of a IDecisionRule behaviour.
 
Methods inherited from class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
createSmartsPattern, getObjectToVerify
 
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

groups

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer[] groups
Constructor Detail

RuleDerivedAromaticAmines

public RuleDerivedAromaticAmines()
Method Detail

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 RuleSMARTSubstructureCDK
Parameters:
mol - org.openscience.cdk.interfaces.AtomContainer
Returns:
rule result, boolean
Throws:
DecisionMethodException

deriveAmine

protected void deriveAmine(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                           org.openscience.cdk.interfaces.IMoleculeSet origin,
                           org.openscience.cdk.interfaces.IMoleculeSet results)

group1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group1()

group2

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer group2()

detachSubstituent

public org.openscience.cdk.interfaces.IMoleculeSet detachSubstituent(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                                                                     org.openscience.cdk.interfaces.IAtomContainer c)


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