mutant.rules

Class SA20_nogen

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleRings

toxTree.tree.rules.RuleRingSubstituents

mutant.rules.SA20_nogen

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter

public class SA20_nogen
extends RuleRingSubstituents
implements IAlertCounter

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IAlertCounter	alertsCounter
static String	SA20_title

Fields inherited from class toxTree.tree.rules.RuleRingSubstituents

analyzeOnlyRingsWithFlagSet, CONDITION_FAILED, CYCLIC_SUBSTITUENT, ERR_PRECONDITION_FAILED, LONGCHAIN_SUBSTITUENT

Fields inherited from class toxTree.tree.rules.RuleSubstructures

ids, MSG_HASGROUP

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

Constructors

Constructor and Description
SA20_nogen()

Method Summary

Modifier and Type	Method and Description
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.
String	getImplementationDetails()
ambit2.rendering.IAtomContainerHighlights	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, getFlag, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet, setFlag, 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, initQuery, 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 String SA20_title

alertsCounter

protected IAlertCounter alertsCounter

Constructor Detail

SA20_nogen

public SA20_nogen()
           throws Exception

Throws:

Exception

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 String allowedSubstituents()

Overrides:

allowedSubstituents in class RuleRingSubstituents

getImplementationDetails

public 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.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRuleHilightHits