verhaar.rules
Class Rule23

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 verhaar.rules.RuleRingMainStrucSubstituents
                                  extended by verhaar.rules.Rule21
                                      extended by verhaar.rules.Rule23
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter

public class Rule23
extends Rule21

Be mononitroaromatics with one or two chlorine substituents and/or alkyl substituents.

Author:
Nina Jeliazkova jeliazkova.nina@gmail.com Modified July 12, 2011
See Also:
Serialized Form

Field Summary
 
Fields inherited from class verhaar.rules.Rule21
alertsCounter, halogenIDs, halogens, halogensCount, maxHalogens, maxNitroGroups, nitroGroupsCount, nitroIDs, phenolIDs
 
Fields inherited from class verhaar.rules.RuleRingMainStrucSubstituents
mainStructure
 
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
Rule23()
           
 
Method Summary
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
           
protected  java.lang.String[] getHalogens()
           
 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 verhaar.rules.Rule21
getImplementationDetails, getMaxHalogens, getMaxNitroGroups, incrementCounter, isImplemented, setMaxHalogens, setMaxNitroGroups, substituentIsAllowed
 
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

Rule23

public Rule23()
Method Detail

getHalogens

protected java.lang.String[] getHalogens()
Overrides:
getHalogens in class Rule21

createMainStructure

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
Overrides:
createMainStructure in class Rule21

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 Rule21
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
Description copied from class: RuleRingAllowedSubstituents
returns true if only allowed substituents are found

Overrides:
verifyRule in class Rule21
Throws:
DecisionMethodException


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