verhaar.rules
Class RuleIonicGroups
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
verhaar.rules.RuleIonicGroups
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter
public class RuleIonicGroups
- extends RuleSubstructures
- implements IAlertCounter
Uses QueryAssociationBond
ro verify if the query compound
has an ionic bond. It relies on the preprocessing by FunctionalGroups.associateIonic(org.openscience.cdk.interfaces.IAtomContainer)
which is called from MolAnalyser
.
- Author:
- Nina Jeliazkova
Modified 2005-10-30
- See Also:
- Serialized Form
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 |
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.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 |
alertsCounter
protected IAlertCounter alertsCounter
RuleIonicGroups
public RuleIonicGroups()
getImplementationDetails
public java.lang.String getImplementationDetails()
- Specified by:
getImplementationDetails
in interface IImplementationDetails
incrementCounter
public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
- Specified by:
incrementCounter
in interface IAlertCounter
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
??
- Specified by:
verifyRule
in interface IDecisionRule
- 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
Copyright © 2004-2012 Ideaconsult Ltd.. All Rights Reserved.