toxTree.tree.cramer
Class RuleMonocarbocyclic

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.AbstractRuleHilightHits
              extended by toxTree.tree.rules.RuleSubstructures
                  extended by toxTree.tree.rules.RuleRings
                      extended by toxTree.tree.rules.RuleRingSubstituents
                          extended by toxTree.tree.rules.RuleRingAllowedSubstituents
                              extended by toxTree.tree.cramer.RuleMonocarbocyclic
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleMonocarbocyclic
extends RuleRingAllowedSubstituents

Rule 24 of the Cramer scheme (see CramerRules)

Version:
0.1, 2005-5-2
Author:
Nina Jeliazkova
See Also:
Serialized Form

Field Summary
 
Fields inherited from class toxTree.tree.rules.RuleRingSubstituents
analyzeOnlyRingsWithFlagSet, CONDITION_FAILED, CYCLIC_SUBSTITUENT, ERR_PRECONDITION_FAILED, flags, LONGCHAIN_SUBSTITUENT
 
Fields inherited from class toxTree.tree.rules.RuleSubstructures
ids, MSG_HASGROUP, query
 
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
RuleMonocarbocyclic()
          Constructor
 
Method Summary
protected  org.openscience.cdk.interfaces.IRingSet hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean isImplemented()
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer selected)
          returns true if only allowed substituents are found
 
Methods inherited from class toxTree.tree.rules.RuleRingAllowedSubstituents
substituentIsAllowed
 
Methods inherited from class toxTree.tree.rules.RuleRingSubstituents
allowedSubstituents, analyze, analyzeOnlyRingsWithFlagSet, clearFlags, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet
 
Methods inherited from class toxTree.tree.rules.RuleSubstructures
addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, removeSubstructure, setIds, setQuery, setSubstructure
 
Methods inherited from class toxTree.tree.AbstractRuleHilightHits
getSelector
 
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
 
Methods inherited from interface toxTree.core.IDecisionRule
addPropertyChangeListener, clearFlags, clone, getEditor, getExampleMolecule, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toString
 

Constructor Detail

RuleMonocarbocyclic

public RuleMonocarbocyclic()
Constructor

Method Detail

isImplemented

public boolean isImplemented()
Specified by:
isImplemented in interface IDecisionRule
Overrides:
isImplemented in class RuleRingAllowedSubstituents
Returns:
false if the rule is not implemented and true if it is

hasRingsToProcess

protected org.openscience.cdk.interfaces.IRingSet hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws DecisionMethodException
Overrides:
hasRingsToProcess in class RuleRings
Throws:
DecisionMethodException

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException
Description copied from class: RuleRingSubstituents
IDecisionRule.verifyRule(IAtomContainer)

Specified by:
verifyRule in interface IDecisionRule
Overrides:
verifyRule in class RuleRingAllowedSubstituents
Parameters:
mol - org.openscience.cdk.interfaces.AtomContainer
Returns:
rule result, boolean
Throws:
DecisionMethodException

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException
Description copied from class: RuleRingAllowedSubstituents
returns true if only allowed substituents are found

Overrides:
verifyRule in class RuleRingAllowedSubstituents
Throws:
DecisionMethodException


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