toxTree.tree.rules

Class RuleCarbohydrate

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleCarbohydrate

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

Direct Known Subclasses:

RuleSimplyBranchedAliphaticHydrocarbon

public class RuleCarbohydrate
extends RuleSubstructures

Verifies if the molecule is a carbohydrate

Author:

Nina Jeliazkova Modified 2005-10-18

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayList<String>	idsAcyclic
protected ArrayList<String>	idsCyclic
protected int	index_alcohol
protected int	index_aldehyde
protected int	index_ether
protected int	index_ketone
static String	MSG_COMMONCARBOHYDRATE
static String	MSG_MANYGROUPSOFAKIND
static String	MSG_NOTACOMMONCARBOHYDRATE

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
RuleCarbohydrate()

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

MSG_COMMONCARBOHYDRATE

public static transient String MSG_COMMONCARBOHYDRATE

MSG_NOTACOMMONCARBOHYDRATE

public static transient String MSG_NOTACOMMONCARBOHYDRATE

MSG_MANYGROUPSOFAKIND

public static transient String MSG_MANYGROUPSOFAKIND

index_alcohol

protected int index_alcohol

index_ether

protected int index_ether

index_aldehyde

protected int index_aldehyde

index_ketone

protected int index_ketone

idsCyclic

protected ArrayList<String> idsCyclic

idsAcyclic

protected ArrayList<String> idsAcyclic

Constructor Detail

RuleCarbohydrate

public RuleCarbohydrate()
                 throws Exception

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,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException

Overrides:

verifyRule in class RuleSubstructures

Throws:

DecisionMethodException

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

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