toxTree.qsar
Class LinearDiscriminantRule
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.qsar.LinearDiscriminantRule
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IDescriptorBased, IImplementationDetails, XMLSerializable
- Direct Known Subclasses:
- RuleDACancerogenicityAromaticAmines, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityAromaticAmines
public abstract class LinearDiscriminantRule
- extends AbstractRule
- implements IImplementationDetails, IDescriptorBased
Uses LinearQSARModel
and returns true if LinearQSARModel.predict(IAtomContainer)
is >= getThreshold()
and false otherwise.
- Author:
- nina
- See Also:
- Serialized Form
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 |
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 |
dictionary
protected static java.util.Hashtable<java.lang.String,java.lang.String> dictionary
model
protected LinearQSARModel model
threshold
protected double threshold
LinearDiscriminantRule
public LinearDiscriminantRule(LinearQSARModel model,
double threshold)
LinearDiscriminantRule
public LinearDiscriminantRule()
getThreshold
public double getThreshold()
setThreshold
public void setThreshold(double threshold)
getModel
public LinearQSARModel getModel()
setModel
public void setModel(LinearQSARModel model)
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
??
- Specified by:
verifyRule
in interface IDecisionRule
- Parameters:
mol
- org.openscience.cdk.interfaces.AtomContainer
- Returns:
- rule result, boolean
- Throws:
DecisionMethodException
createException
protected abstract DRuleException createException(ambit2.base.exceptions.QSARModelException x)
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
compare
protected boolean compare(double value,
double threshold)
hint
protected java.lang.String hint()
getImplementationDetails
public java.lang.String getImplementationDetails()
- Specified by:
getImplementationDetails
in interface IImplementationDetails
isCalculated
public boolean isCalculated(java.lang.String name)
- Specified by:
isCalculated
in interface IDescriptorBased
setCalculated
public void setCalculated(org.openscience.cdk.qsar.IMolecularDescriptor descriptor,
java.lang.String name,
boolean calculated)
- Specified by:
setCalculated
in interface IDescriptorBased
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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