toxTree.tree.rules

Class RuleRingAllowedSubstituents

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

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

Direct Known Subclasses:

Rule143, RuleCyclopropaneEtc, RuleMonocarbocyclic, RuleRingMainStrucSubstituents, RuleSomeBenzeneDerivatives

public class RuleRingAllowedSubstituents
extends RuleRingSubstituents

A rule to analyze ring substituents

Author:

Nina Jeliazkova Modified 2005-8-17

See Also:

Serialized Form

Field Summary

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
RuleRingAllowedSubstituents()

Method Summary

Modifier and Type	Method and Description
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)
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, getFlag, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet, setFlag

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.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

Constructor Detail

RuleRingAllowedSubstituents

public RuleRingAllowedSubstituents()
                            throws Exception

Throws:

Exception

Method Detail

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

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

Specified by:

substituentIsAllowed in class RuleRingSubstituents

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 RuleRingSubstituents

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

returns true if only allowed substituents are found

Overrides:

verifyRule in class RuleRingSubstituents

Throws:

DecisionMethodException