toxTree.tree.cramer
Class RuleSomeBenzeneDerivatives

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.RuleSomeBenzeneDerivatives
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleSomeBenzeneDerivatives
extends RuleRingAllowedSubstituents

Rule 6 of the Cramer scheme (see CramerRules)

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

Field Summary
protected  java.util.ArrayList alkoxyIDs
           
protected  java.util.ArrayList chIDs
           
protected  java.util.ArrayList hydroxyIDs
           
protected  int index_alkoxy
           
protected  int index_ester
           
protected  int index_hydrocarbon
           
protected  int index_hydroxy
           
protected  int index_hydroxy1
           
static java.lang.String MSG_ALKOXYPARACH
           
static java.lang.String MSG_BENZENESUBSTITUENT
           
protected  int[] places
           
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring6
           
 
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
RuleSomeBenzeneDerivatives()
          Constructor
 
Method Summary
protected  org.openscience.cdk.interfaces.IRingSet hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 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)
 
Methods inherited from class toxTree.tree.rules.RuleRingAllowedSubstituents
verifyRule
 
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
 

Field Detail

MSG_ALKOXYPARACH

public static final transient java.lang.String MSG_ALKOXYPARACH
See Also:
Constant Field Values

MSG_BENZENESUBSTITUENT

public static final transient java.lang.String MSG_BENZENESUBSTITUENT
See Also:
Constant Field Values

index_hydroxy1

protected int index_hydroxy1

index_hydroxy

protected int index_hydroxy

index_ester

protected int index_ester

index_alkoxy

protected int index_alkoxy

index_hydrocarbon

protected int index_hydrocarbon

chIDs

protected java.util.ArrayList chIDs

hydroxyIDs

protected java.util.ArrayList hydroxyIDs

alkoxyIDs

protected java.util.ArrayList alkoxyIDs

places

protected int[] places

ring6

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring6
Constructor Detail

RuleSomeBenzeneDerivatives

public RuleSomeBenzeneDerivatives()
Constructor

Method Detail

hasRingsToProcess

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

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

Overrides:
substituentIsAllowed in class RuleRingAllowedSubstituents
Throws:
DecisionMethodException

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

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


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