toxTree.tree.rules
Class RuleCarbohydrate

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.AbstractRuleHilightHits
              extended by toxTree.tree.rules.RuleSubstructures
                  extended by toxTree.tree.rules.RuleCarbohydrate
All Implemented Interfaces:
java.io.Serializable, java.lang.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
protected  java.util.ArrayList idsAcyclic
           
protected  java.util.ArrayList idsCyclic
           
protected  int index_alcohol
           
protected  int index_aldehyde
           
protected  int index_ether
           
protected  int index_ketone
           
static java.lang.String MSG_COMMONCARBOHYDRATE
           
static java.lang.String MSG_MANYGROUPSOFAKIND
           
static java.lang.String MSG_NOTACOMMONCARBOHYDRATE
           
 
Fields inherited from class toxTree.tree.rules.RuleSubstructures
ids, MSG_HASGROUP, query
 
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
RuleCarbohydrate()
           
 
Method Summary
 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 java.lang.String MSG_COMMONCARBOHYDRATE

MSG_NOTACOMMONCARBOHYDRATE

public static transient java.lang.String MSG_NOTACOMMONCARBOHYDRATE

MSG_MANYGROUPSOFAKIND

public static transient java.lang.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 java.util.ArrayList idsCyclic

idsAcyclic

protected java.util.ArrayList idsAcyclic
Constructor Detail

RuleCarbohydrate

public RuleCarbohydrate()
Method Detail

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


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