eye.rules
Class Rule13_AliphaticMonoalcohols

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by eye.rules.Rule13_AliphaticMonoalcohols
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, XMLSerializable
Direct Known Subclasses:
Rule30, Rule38

public class Rule13_AliphaticMonoalcohols
extends AbstractRule

A Lactams

Author:
Nina Jeliazkova nina@acad.bg, Martin Martinov Modified Dec 17, 2006
See Also:
Serialized Form

Field Summary
protected  ambit2.smarts.query.SmartsPatternCDK smartsPattern
           
 
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
Rule13_AliphaticMonoalcohols()
           
 
Method Summary
protected  int countChain(org.openscience.cdk.interfaces.IMolecule m)
           
protected  org.openscience.cdk.interfaces.IMoleculeSet extractChains(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.List<java.util.List<java.lang.Integer>> matchedAtoms)
           
protected  int getMaxChainLength()
           
protected  int getMinChainLength()
           
 ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
           
 boolean isImplemented()
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          This is the core of a IDecisionRule behaviour.
 
Methods inherited from class toxTree.tree.AbstractRule
addPropertyChangeListener, clearFlags, clone, createRule, equals, 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
 

Field Detail

smartsPattern

protected ambit2.smarts.query.SmartsPatternCDK smartsPattern
Constructor Detail

Rule13_AliphaticMonoalcohols

public Rule13_AliphaticMonoalcohols()
Method Detail

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

countChain

protected int countChain(org.openscience.cdk.interfaces.IMolecule m)
                  throws DecisionMethodException
Throws:
DecisionMethodException

getMinChainLength

protected int getMinChainLength()

getMaxChainLength

protected int getMaxChainLength()

extractChains

protected org.openscience.cdk.interfaces.IMoleculeSet extractChains(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                    java.util.List<java.util.List<java.lang.Integer>> matchedAtoms)
                                                             throws DecisionMethodException
Throws:
DecisionMethodException

isImplemented

public boolean isImplemented()
Specified by:
isImplemented in interface IDecisionRule
Overrides:
isImplemented in class AbstractRule
Returns:
false if the rule is not implemented and true if it is

getSelector

public ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
Specified by:
getSelector in interface IDecisionRule
Overrides:
getSelector in class AbstractRule


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