eye.rules

Class Rule13_AliphaticMonoalcohols

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

eye.rules.Rule13_AliphaticMonoalcohols

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, XMLSerializable

Direct Known Subclasses:

Rule30, Rule38

public class Rule13_AliphaticMonoalcohols
extends AbstractRule

A Lactams

Author:

Nina Jeliazkova nina@acad.bg, Martin Martinov Modified Dec 17, 2006

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ambit2.smarts.query.SmartsPatternCDK	smartsPattern

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
Rule13_AliphaticMonoalcohols()

Method Summary

Modifier and Type	Method and Description
protected int	countChain(org.openscience.cdk.interfaces.IAtomContainer m)
protected org.openscience.cdk.interfaces.IAtomContainerSet	extractChains(org.openscience.cdk.interfaces.IAtomContainer mol, List<List<Integer>> matchedAtoms)
protected int	getMaxChainLength()
protected int	getMinChainLength()
ambit2.rendering.IAtomContainerHighlights	getSelector()
boolean	isImplemented()
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, equals, 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

Field Detail

smartsPattern

protected ambit2.smarts.query.SmartsPatternCDK smartsPattern

Constructor Detail

Rule13_AliphaticMonoalcohols

public Rule13_AliphaticMonoalcohols()

Method Detail

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

countChain

protected int countChain(org.openscience.cdk.interfaces.IAtomContainer m)
                  throws DecisionMethodException

Throws:

DecisionMethodException

getMinChainLength

protected int getMinChainLength()

getMaxChainLength

protected int getMaxChainLength()

extractChains

protected org.openscience.cdk.interfaces.IAtomContainerSet extractChains(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                         List<List<Integer>> matchedAtoms)
                                                                  throws DecisionMethodException

Throws:

DecisionMethodException

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class AbstractRule

Returns:

false if the rule is not implemented and true if it is

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule