mutant.rules
Class RuleDAMutagenicityAromaticAmines

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.qsar.LinearDiscriminantRule
              extended by mutant.rules.RuleDAMutagenicityAromaticAmines
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IDescriptorBased, IImplementationDetails, XMLSerializable

public class RuleDAMutagenicityAromaticAmines
extends LinearDiscriminantRule

Returns true if structure is predicted as mutagen , based on linear discriminant analysis. AM1

 w = - 2.85 HOMO + 1.84 LUMO + 0.70 MR2 + 0.69 MR3 + 1.90 MR6  +  3.36 Idist 
 w >  25.04  non-mutagens
 w <  25.04  mutagens
 
21 Sep 2007 - the equation was changed (RE Prof. R.Benigni) in order to use PM3 instead of AM1 calculations.
 w = - 3.14 HOMO + 1.76 LUMO + 0.62 MR2 + 0.75 MR3 + 1.88 MR6  +  3.75
> Idist     (8ter)
> w(mean,Class1) =  28.42       N1 = 47  (non-mutagens)
> w(mean,Class2) =  26.44       N2 = 64  (mutagens)
> Threshold =  27.43 
 

See Also:
Serialized Form

Field Summary
 
Fields inherited from class toxTree.qsar.LinearDiscriminantRule
dictionary, model, threshold
 
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
RuleDAMutagenicityAromaticAmines()
           
 
Method Summary
protected  boolean compare(double value, double threshold)
           
protected  DRuleException createException(ambit2.base.exceptions.QSARModelException x)
           
static LinearQSARModel createMutagenicityofAromaticAminesModel()
           
 java.lang.String getImplementationDetails()
           
 
Methods inherited from class toxTree.qsar.LinearDiscriminantRule
getModel, getSelector, getThreshold, hint, isCalculated, isImplemented, setCalculated, setModel, setThreshold, verifyRule
 
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
 

Constructor Detail

RuleDAMutagenicityAromaticAmines

public RuleDAMutagenicityAromaticAmines()
                                 throws java.lang.Exception
Throws:
java.lang.Exception
Method Detail

createMutagenicityofAromaticAminesModel

public static LinearQSARModel createMutagenicityofAromaticAminesModel()
                                                               throws java.lang.Exception
Throws:
java.lang.Exception

compare

protected boolean compare(double value,
                          double threshold)
Overrides:
compare in class LinearDiscriminantRule

getImplementationDetails

public java.lang.String getImplementationDetails()
Specified by:
getImplementationDetails in interface IImplementationDetails
Overrides:
getImplementationDetails in class LinearDiscriminantRule

createException

protected DRuleException createException(ambit2.base.exceptions.QSARModelException x)
Specified by:
createException in class LinearDiscriminantRule


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