toxTree.tree.rules

Class RuleRingSubstituents

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleRings

toxTree.tree.rules.RuleRingSubstituents

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

Direct Known Subclasses:

RuleOnlyFuncGroupsQ30, RuleRingAllowedSubstituents, RuleRingOtherThanAllowedSubstituents, SA20_nogen

public abstract class RuleRingSubstituents
extends RuleRings

A rule to analyze ring substituents

Author:

Nina Jeliazkova Modified 2005-8-17

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	analyzeOnlyRingsWithFlagSet
static String	CONDITION_FAILED
static String	CYCLIC_SUBSTITUENT
static String	ERR_PRECONDITION_FAILED
static String	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
RuleRingSubstituents()

Method Summary

Modifier and Type	Method and Description
String	allowedSubstituents()
protected boolean	analyze(org.openscience.cdk.interfaces.IRing r)
boolean	analyzeOnlyRingsWithFlagSet()
void	clearFlags()
boolean	getFlag(int mask)
void	setAnalyzeAromatic(boolean flag)
void	setAnalyzeHeterocyclic(boolean flag)
void	setAnalyzeOnlyRingsWithFlagSet(boolean analyzeOnlyRingsWithFlagSet)
void	setFlag(int mask, boolean value)
abstract 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)

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, isImplemented, 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

ERR_PRECONDITION_FAILED

public static String ERR_PRECONDITION_FAILED

CONDITION_FAILED

public static String CONDITION_FAILED

CYCLIC_SUBSTITUENT

public static String CYCLIC_SUBSTITUENT

LONGCHAIN_SUBSTITUENT

public static String LONGCHAIN_SUBSTITUENT

analyzeOnlyRingsWithFlagSet

protected boolean analyzeOnlyRingsWithFlagSet

Constructor Detail

RuleRingSubstituents

public RuleRingSubstituents()
                     throws Exception

Throws:

Exception

Method Detail

setFlag

public void setFlag(int mask,
                    boolean value)

getFlag

public boolean getFlag(int mask)

analyze

protected boolean analyze(org.openscience.cdk.interfaces.IRing r)

substituentIsAllowed

public abstract boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
                                             int[] place)
                                      throws DecisionMethodException

returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class

Throws:

DecisionMethodException

clearFlags

public void clearFlags()

setAnalyzeHeterocyclic

public void setAnalyzeHeterocyclic(boolean flag)

setAnalyzeAromatic

public void setAnalyzeAromatic(boolean flag)

analyzeOnlyRingsWithFlagSet

public boolean analyzeOnlyRingsWithFlagSet()

Returns:

Returns the analyzeOnlyRingsWithFlagSet.

setAnalyzeOnlyRingsWithFlagSet

public void setAnalyzeOnlyRingsWithFlagSet(boolean analyzeOnlyRingsWithFlagSet)

Parameters:

analyzeOnlyRingsWithFlagSet - The analyzeOnlyRingsWithFlagSet to set.

allowedSubstituents

public String allowedSubstituents()

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException

IDecisionRule.verifyRule(IAtomContainer)

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

Overrides:

verifyRule in class RuleSubstructures

Throws:

DecisionMethodException