toxTree.tree.cramer
Class RuleAliphaticWithSomeFuncGroups

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.cramer.RuleAliphaticWithSomeFuncGroups
All Implemented Interfaces:
java.io.Serializable, java.lang.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
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, 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
RuleAliphaticWithSomeFuncGroups()
          Constructor
 
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

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()
Constructor

Method Detail

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


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