mic.rules
Class SA10

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 toxTree.tree.rules.StructureAlertCDK
                      extended by mic.rules.SA10
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IAlertCounter, IRuleSMARTSubstructures

public class SA10
extends StructureAlertCDK

See Also:
Serialized Form

Field Summary
protected static java.lang.String AB_UNSATURATED_CARBONYLS
           
protected static java.lang.String AB_UNSATURATED_CARBONYLS_SMARTS
           
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer query
           
 
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
SA10()
           
 
Method Summary
 boolean CH6SubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)
           
 org.openscience.cdk.interfaces.IMoleculeSet detachSubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          This is the core of a IDecisionRule behaviour.
 
Methods inherited from class toxTree.tree.rules.StructureAlertCDK
getImplementationDetails, incrementCounter
 
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, 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

AB_UNSATURATED_CARBONYLS

protected static java.lang.String AB_UNSATURATED_CARBONYLS

AB_UNSATURATED_CARBONYLS_SMARTS

protected static java.lang.String AB_UNSATURATED_CARBONYLS_SMARTS

query

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer query
Constructor Detail

SA10

public SA10()
     throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException
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 StructureAlertCDK
Parameters:
mol - org.openscience.cdk.interfaces.AtomContainer
Returns:
rule result, boolean
Throws:
DecisionMethodException

detachSubstituentAtBetaCarbon

public org.openscience.cdk.interfaces.IMoleculeSet detachSubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)

CH6SubstituentAtBetaCarbon

public boolean CH6SubstituentAtBetaCarbon(org.openscience.cdk.interfaces.IAtomContainer c)


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