verhaar.rules
Class Rule21

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
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter
Direct Known Subclasses:
Rule22, Rule23, Rule25

public class Rule21
extends RuleRingMainStrucSubstituents
implements IAlertCounter

Non- or weakly acidic phenols.

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

Field Summary
protected  IAlertCounter alertsCounter
           
protected  java.util.ArrayList halogenIDs
           
protected  java.lang.String[] halogens
           
protected  int halogensCount
           
protected  int maxHalogens
           
protected  int maxNitroGroups
           
protected  int nitroGroupsCount
           
protected  java.util.ArrayList nitroIDs
           
protected  java.util.ArrayList 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
Rule21()
           
 
Method Summary
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
           
protected  java.lang.String[] getHalogens()
           
 java.lang.String getImplementationDetails()
           
 int getMaxHalogens()
           
 int getMaxNitroGroups()
           
 void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean isImplemented()
           
 void setMaxHalogens(int maxHalogens)
           
 void setMaxNitroGroups(int maxNitroGroups)
           
 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
 

Field Detail

alertsCounter

protected IAlertCounter alertsCounter

nitroGroupsCount

protected transient int nitroGroupsCount

halogensCount

protected transient int halogensCount

halogens

protected transient java.lang.String[] halogens

nitroIDs

protected java.util.ArrayList nitroIDs

phenolIDs

protected java.util.ArrayList phenolIDs

halogenIDs

protected java.util.ArrayList halogenIDs

maxHalogens

protected int maxHalogens

maxNitroGroups

protected int maxNitroGroups
Constructor Detail

Rule21

public Rule21()
Method Detail

getHalogens

protected java.lang.String[] getHalogens()

createMainStructure

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
Specified by:
createMainStructure in class RuleRingMainStrucSubstituents

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 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 RuleRingAllowedSubstituents
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

getMaxHalogens

public int getMaxHalogens()

setMaxHalogens

public void setMaxHalogens(int maxHalogens)

getMaxNitroGroups

public int getMaxNitroGroups()

setMaxNitroGroups

public void setMaxNitroGroups(int maxNitroGroups)

getImplementationDetails

public java.lang.String getImplementationDetails()
Specified by:
getImplementationDetails in interface IImplementationDetails

incrementCounter

public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
Specified by:
incrementCounter in interface IAlertCounter


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