toxtree.plugins.smartcyp.rules
Class MetaboliteGenerator

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxtree.plugins.smartcyp.rules.MetaboliteGenerator
All Implemented Interfaces:
ambit2.smarts.IAcceptable, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IMetaboliteGenerator, XMLSerializable
Direct Known Subclasses:
SMARTCYPRuleRank1

public abstract class MetaboliteGenerator
extends AbstractRule
implements IMetaboliteGenerator, ambit2.smarts.IAcceptable

See Also:
Serialized Form

Field Summary
protected  java.util.ResourceBundle bundle
           
protected  int rank
           
protected  ambit2.smarts.SMIRKSManager smrkMan
           
 
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
MetaboliteGenerator()
           
 
Method Summary
 boolean accept(java.util.Vector<org.openscience.cdk.interfaces.IAtom> atoms)
           
 java.lang.String getHelp(RuleResult ruleresult)
           
 org.openscience.cdk.interfaces.IAtomContainerSet getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant, RuleResult ruleResult)
           
 int getRank()
           
 void setRank(int rank)
           
 
Methods inherited from class toxTree.tree.AbstractRule
addPropertyChangeListener, clearFlags, clone, createRule, equals, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isImplemented, 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
verifyRule
 

Field Detail

smrkMan

protected transient ambit2.smarts.SMIRKSManager smrkMan

rank

protected int rank

bundle

protected transient java.util.ResourceBundle bundle
Constructor Detail

MetaboliteGenerator

public MetaboliteGenerator()
Method Detail

getRank

public int getRank()

setRank

public void setRank(int rank)

getProducts

public org.openscience.cdk.interfaces.IAtomContainerSet getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant,
                                                                    RuleResult ruleResult)
                                                             throws java.lang.Exception
Specified by:
getProducts in interface IMetaboliteGenerator
Throws:
java.lang.Exception

accept

public boolean accept(java.util.Vector<org.openscience.cdk.interfaces.IAtom> atoms)
Specified by:
accept in interface ambit2.smarts.IAcceptable

getHelp

public java.lang.String getHelp(RuleResult ruleresult)
Specified by:
getHelp in interface IMetaboliteGenerator


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