toxTree.tree.rules
Class RuleRingSubstituents

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
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable
Direct Known Subclasses:
RuleOnlyFuncGroupsQ30, RuleRingAllowedSubstituents, RuleRingOtherThanAllowedSubstituents, SA20_nogen

public abstract class RuleRingSubstituents
extends RuleRings

A rule to analyze ring substituents

Author:
Nina Jeliazkova Modified 2005-8-17
See Also:
Serialized Form

Field Summary
protected  boolean analyzeOnlyRingsWithFlagSet
           
static java.lang.String CONDITION_FAILED
           
static java.lang.String CYCLIC_SUBSTITUENT
           
static java.lang.String ERR_PRECONDITION_FAILED
           
protected  boolean[] flags
           
static java.lang.String 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
RuleRingSubstituents()
           
 
Method Summary
 java.lang.String allowedSubstituents()
           
protected  boolean analyze(org.openscience.cdk.interfaces.IRing r)
           
 boolean analyzeOnlyRingsWithFlagSet()
           
 void clearFlags()
           
 void setAnalyzeAromatic(boolean flag)
           
 void setAnalyzeHeterocyclic(boolean flag)
           
 void setAnalyzeOnlyRingsWithFlagSet(boolean analyzeOnlyRingsWithFlagSet)
           
abstract  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)
           
 
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, isImplemented, 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

ERR_PRECONDITION_FAILED

public static java.lang.String ERR_PRECONDITION_FAILED

CONDITION_FAILED

public static java.lang.String CONDITION_FAILED

CYCLIC_SUBSTITUENT

public static java.lang.String CYCLIC_SUBSTITUENT

LONGCHAIN_SUBSTITUENT

public static java.lang.String LONGCHAIN_SUBSTITUENT

flags

protected boolean[] flags

analyzeOnlyRingsWithFlagSet

protected boolean analyzeOnlyRingsWithFlagSet
Constructor Detail

RuleRingSubstituents

public RuleRingSubstituents()
Method Detail

analyze

protected boolean analyze(org.openscience.cdk.interfaces.IRing r)

substituentIsAllowed

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

Throws:
DecisionMethodException

clearFlags

public void clearFlags()

setAnalyzeHeterocyclic

public void setAnalyzeHeterocyclic(boolean flag)

setAnalyzeAromatic

public void setAnalyzeAromatic(boolean flag)

analyzeOnlyRingsWithFlagSet

public boolean analyzeOnlyRingsWithFlagSet()
Returns:
Returns the analyzeOnlyRingsWithFlagSet.

setAnalyzeOnlyRingsWithFlagSet

public void setAnalyzeOnlyRingsWithFlagSet(boolean analyzeOnlyRingsWithFlagSet)
Parameters:
analyzeOnlyRingsWithFlagSet - The analyzeOnlyRingsWithFlagSet to set.

allowedSubstituents

public java.lang.String allowedSubstituents()

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException
IDecisionRule.verifyRule(IAtomContainer)

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
Overrides:
verifyRule in class RuleSubstructures
Throws:
DecisionMethodException


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