toxtree.plugins.ames.rules

Class RuleDAMutagenicityAromaticAmines

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.qsar.LinearDiscriminantRule

toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines

All Implemented Interfaces:

Serializable, 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

Constructors

Constructor and Description
RuleDAMutagenicityAromaticAmines()

Method Summary

Modifier and Type	Method and Description
protected boolean	compare(double value, double threshold)
protected DRuleException	createException(ambit2.base.exceptions.QSARModelException x)
static LinearQSARModel	createMutagenicityofAromaticAminesModel()
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 Exception

Throws:

Exception

Method Detail

createMutagenicityofAromaticAminesModel

public static LinearQSARModel createMutagenicityofAromaticAminesModel()
                                                               throws Exception

Throws:

Exception

compare

protected boolean compare(double value,
                          double threshold)

Overrides:

compare in class LinearDiscriminantRule

getImplementationDetails

public 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