toxtree.plugins.kroes.rules
Class RuleKroesFig1Q1

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.plugins.kroes.rules.RuleKroesFig1Q1
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleKroesFig1Q1
extends RuleSubstructures

TODO refactor with SMARTS

Author:
nina
See Also:
Serialized Form

Field Summary
static java.lang.String config
           
static java.lang.String[] halogens
           
static java.lang.String[] me_essential
           
static java.lang.String[] me_nonessential
           
 
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
RuleKroesFig1Q1()
           
RuleKroesFig1Q1(java.io.File file)
           
RuleKroesFig1Q1(java.io.InputStream stream, java.lang.String format)
           
 
Method Summary
static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
           
protected static java.io.InputStream getConfiguration()
           
protected  void init()
           
 boolean isImplemented()
           
protected  void print(org.openscience.cdk.interfaces.IAtomContainer a)
           
protected  void readStream(java.io.InputStream fStream, java.lang.String format)
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          This is the core of a IDecisionRule behaviour.
 
Methods inherited from class toxTree.tree.rules.RuleSubstructures
addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, removeSubstructure, setIds, setQuery, setSubstructure, verifyRule
 
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

halogens

public static transient java.lang.String[] halogens

me_essential

public static transient java.lang.String[] me_essential

me_nonessential

public static transient java.lang.String[] me_nonessential

config

public static transient java.lang.String config
Constructor Detail

RuleKroesFig1Q1

public RuleKroesFig1Q1()

RuleKroesFig1Q1

public RuleKroesFig1Q1(java.io.InputStream stream,
                       java.lang.String format)

RuleKroesFig1Q1

public RuleKroesFig1Q1(java.io.File file)
Method Detail

init

protected void init()

readStream

protected void readStream(java.io.InputStream fStream,
                          java.lang.String format)

createQueryContainer

public static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)

getConfiguration

protected static java.io.InputStream getConfiguration()

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

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??

Parameters:
mol - org.openscience.cdk.interfaces.AtomContainer
Returns:
rule result, boolean
Throws:
DecisionMethodException

print

protected void print(org.openscience.cdk.interfaces.IAtomContainer a)


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