verhaar.rules

Class Rule143

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleRings

toxTree.tree.rules.RuleRingSubstituents

toxTree.tree.rules.RuleRingAllowedSubstituents

verhaar.rules.Rule143

All Implemented Interfaces:

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

Direct Known Subclasses:

Rule144

public class Rule143
extends RuleRingAllowedSubstituents
implements IAlertCounter

Monocyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with rule Rule141.

Author:

Nina Jeliazkova jeliazkova.nina@gmail.com Modified July 12, 2011

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IAlertCounter	alertsCounter
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	x

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
Rule143()

Method Summary

Modifier and Type	Method and Description
String	getImplementationDetails()
protected org.openscience.cdk.interfaces.IRingSet	hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
void	incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
protected QueryAtomContainers	initQuery()
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, getFlag, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet, setFlag

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

x

protected transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer x

Constructor Detail

Rule143

public Rule143()
        throws Exception

Throws:

Exception

Method Detail

initQuery

protected QueryAtomContainers initQuery()
                                 throws Exception

Overrides:

initQuery in class RuleSubstructures

Throws:

Exception

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

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

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

incrementCounter

public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

incrementCounter in interface IAlertCounter

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails