toxTree.tree.cramer

Class RuleAliphaticWithSomeFuncGroups

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleAliphaticWithSomeFuncGroups
extends RuleSubstructures

Rule 20 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 static int	acetal_id
protected static int	alcohol_id
protected static int	aldehyde_id
protected static int	aminePrimary_id
protected static int	amineTertiary_id
protected static int	carbonate_id
protected static int	carboxylicacid_id
protected static int	ester_id
protected static int	ketone_id
protected static int	mercaptan_id
protected static int	sulphide_id
protected static int	thioester_id

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
RuleAliphaticWithSomeFuncGroups() Constructor

Method Summary

Modifier and Type	Method and Description
protected QueryAtomContainers	initQuery()
boolean	isImplemented()
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.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

carbonate_id

protected static int carbonate_id

carboxylicacid_id

protected static int carboxylicacid_id

ester_id

protected static int ester_id

aldehyde_id

protected static int aldehyde_id

alcohol_id

protected static int alcohol_id

ketone_id

protected static int ketone_id

acetal_id

protected static int acetal_id

thioester_id

protected static int thioester_id

sulphide_id

protected static int sulphide_id

mercaptan_id

protected static int mercaptan_id

aminePrimary_id

protected static int aminePrimary_id

amineTertiary_id

protected static int amineTertiary_id

Constructor Detail

RuleAliphaticWithSomeFuncGroups

public RuleAliphaticWithSomeFuncGroups()
                                throws Exception

Constructor

Throws:

Exception

Method Detail

initQuery

protected QueryAtomContainers initQuery()
                                 throws Exception

Overrides:

initQuery in class RuleSubstructures

Throws:

Exception

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

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