toxTree.tree.rules
Class RuleRingAllowedSubstituents

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
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable
Direct Known Subclasses:
Rule143, RuleCyclopropaneEtc, RuleMonocarbocyclic, RuleRingMainStrucSubstituents, RuleSomeBenzeneDerivatives

public class RuleRingAllowedSubstituents
extends RuleRingSubstituents

A rule to analyze ring substituents

Author:
Nina Jeliazkova Modified 2005-8-17
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
RuleRingAllowedSubstituents()
           
 
Method Summary
 boolean isImplemented()
           
 boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
          returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
          returns true if only allowed substituents are found
 
Methods inherited from class toxTree.tree.rules.RuleRingSubstituents
allowedSubstituents, analyze, analyzeOnlyRingsWithFlagSet, clearFlags, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet
 
Methods inherited from class toxTree.tree.rules.RuleRings
hasRingsToProcess
 
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

RuleRingAllowedSubstituents

public RuleRingAllowedSubstituents()
Method Detail

isImplemented

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

substituentIsAllowed

public boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
                                    int[] place)
                             throws DecisionMethodException
Description copied from class: RuleRingSubstituents
returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class

Specified by:
substituentIsAllowed in class RuleRingSubstituents
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 RuleRingSubstituents
Parameters:
mol - org.openscience.cdk.interfaces.AtomContainer
Returns:
rule result, boolean
Throws:
DecisionMethodException

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException
returns true if only allowed substituents are found

Overrides:
verifyRule in class RuleRingSubstituents
Throws:
DecisionMethodException


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