mutant.rules
Class SA20_nogen

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 mutant.rules.SA20_nogen
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter

public class SA20_nogen
extends RuleRingSubstituents
implements IAlertCounter

See Also:
Serialized Form

Field Summary
protected  IAlertCounter alertsCounter
           
static java.lang.String SA20_title
           
 
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
SA20_nogen()
           
 
Method Summary
 java.lang.String allowedSubstituents()
           
protected  boolean analyze(org.openscience.cdk.interfaces.IRing r)
          Initialize halogen counts to zero and returns true if the ring consists of single bonds only.
 java.lang.String getImplementationDetails()
           
 ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
           
 void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean isImplemented()
           
 boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
          Only counts halogens directly connected to the ring and returns true always.
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 
Methods inherited from class toxTree.tree.rules.RuleRingSubstituents
analyzeOnlyRingsWithFlagSet, clearFlags, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet, verifyRule
 
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.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, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toString
 

Field Detail

SA20_title

public static java.lang.String SA20_title

alertsCounter

protected IAlertCounter alertsCounter
Constructor Detail

SA20_nogen

public SA20_nogen()
Method Detail

incrementCounter

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

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException
Overrides:
verifyRule in class RuleRingSubstituents
Throws:
DecisionMethodException

analyze

protected boolean analyze(org.openscience.cdk.interfaces.IRing r)
Initialize halogen counts to zero and returns true if the ring consists of single bonds only.

Overrides:
analyze in class RuleRingSubstituents

substituentIsAllowed

public boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
                                    int[] place)
                             throws DecisionMethodException
Only counts halogens directly connected to the ring and returns true always.

Specified by:
substituentIsAllowed in class RuleRingSubstituents
Throws:
DecisionMethodException

allowedSubstituents

public java.lang.String allowedSubstituents()
Overrides:
allowedSubstituents in class RuleRingSubstituents

getImplementationDetails

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

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

getSelector

public ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
Specified by:
getSelector in interface IDecisionRule
Overrides:
getSelector in class AbstractRuleHilightHits


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