toxtree.plugins.kroes.rules

Class RuleKroesFig1Q1

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxtree.plugins.kroes.rules.RuleKroesFig1Q1

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleKroesFig1Q1
extends RuleSubstructures

TODO refactor with SMARTS

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	config
static String[]	halogens
static String[]	me_essential
static String[]	me_nonessential

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
RuleKroesFig1Q1()
RuleKroesFig1Q1(File file)
RuleKroesFig1Q1(InputStream stream, String format)

Method Summary

Modifier and Type	Method and Description
static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
protected static InputStream	getConfiguration()
protected void	init()
boolean	isImplemented()
protected void	readStream(InputStream fStream, String format)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class toxTree.tree.rules.RuleSubstructures

addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, initQuery, removeSubstructure, setIds, setQuery, setSubstructure, verifyRule

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

halogens

public static transient String[] halogens

me_essential

public static transient String[] me_essential

me_nonessential

public static transient String[] me_nonessential

config

public static transient String config

Constructor Detail

RuleKroesFig1Q1

public RuleKroesFig1Q1()
                throws Exception

Throws:

Exception

RuleKroesFig1Q1

public RuleKroesFig1Q1(InputStream stream,
                       String format)
                throws Exception

Throws:

Exception

RuleKroesFig1Q1

public RuleKroesFig1Q1(File file)
                throws Exception

Throws:

Exception

Method Detail

init

protected void init()

readStream

protected void readStream(InputStream fStream,
                          String format)

createQueryContainer

public static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)

getConfiguration

protected static InputStream getConfiguration()

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

verifyRule

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

Description copied from interface: IDecisionRule

This is the core of a IDecisionRule behaviour. The method returns true if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer and FALSE if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer??

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException