toxTree.tree.cramer

Class RuleSomeBenzeneDerivatives

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

toxTree.tree.cramer.RuleSomeBenzeneDerivatives

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleSomeBenzeneDerivatives
extends RuleRingAllowedSubstituents

Rule 6 of the Cramer scheme (see CramerRules)

Version:

0.1, 2005-5-2

Author:

Nina Jeliazkova

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayList	alkoxyIDs
protected ArrayList	chIDs
protected ArrayList	hydroxyIDs
protected int	index_alkoxy
protected int	index_ester
protected int	index_hydrocarbon
protected int	index_hydroxy
protected int	index_hydroxy1
static String	MSG_ALKOXYPARACH
static String	MSG_BENZENESUBSTITUENT
protected int[]	places
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	ring6

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
RuleSomeBenzeneDerivatives() Constructor

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IRingSet	hasRingsToProcess(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

MSG_ALKOXYPARACH

public static final transient String MSG_ALKOXYPARACH

See Also:

Constant Field Values

MSG_BENZENESUBSTITUENT

public static final transient String MSG_BENZENESUBSTITUENT

See Also:

Constant Field Values

index_hydroxy1

protected int index_hydroxy1

index_hydroxy

protected int index_hydroxy

index_ester

protected int index_ester

index_alkoxy

protected int index_alkoxy

index_hydrocarbon

protected int index_hydrocarbon

chIDs

protected ArrayList chIDs

hydroxyIDs

protected ArrayList hydroxyIDs

alkoxyIDs

protected ArrayList alkoxyIDs

places

protected int[] places

ring6

protected transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring6

Constructor Detail

RuleSomeBenzeneDerivatives

public RuleSomeBenzeneDerivatives()
                           throws Exception

Constructor

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

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

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