@PublicAPI public class BCUTParameters extends MDParameters
BCUT
descriptor class.
The native format of the parameter configuration is XML.asymmetryFactors, cellSize, cellwiseWeights, configFilePath, currentMetricIndex, data, decForm, DEFAULT_ASYMMETRY_FACTOR, DEFAULT_OUTPUT_PRECISION, DEFAULT_SCALE_FACTOR, DEFAULT_WEIGHT, defaultWeight, document, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights
Constructor and Description |
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BCUTParameters()
Creates an empty object.
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BCUTParameters(java.io.File configFile)
Creates a new object based on a given configuration file.
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BCUTParameters(java.lang.String XMLconfig)
Creates a new object based on a given configuration string.
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Modifier and Type | Method and Description |
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void |
fromString(java.lang.String parameterString)
Sets parameters from a string representation.
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protected java.lang.String[] |
generate(Molecule m,
MolecularDescriptor bc)
Calls the descriptor generator for the molecule provided and stores
result (the descriptor) in the
MolecularDescriptor
object. |
java.lang.String |
getDefaultDocumentFrame()
Gets the default XML configuration string.
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int |
getHighestEigenvaluesCount(int idx)
Gets the number of highest eigenvalues calculated.
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int |
getLowestEigenvaluesCount(int idx)
Gets the number of lowest eigenvalues calculated.
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protected int |
getNumberOfWeights(int parametrizedMetricIndex)
Gets the number of weight factors used by the specified metric.
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java.lang.String |
getType(int idx)
Gets the type of the BCUT descriptor.
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int |
getTypeCount()
Gets the count of descriptor types.
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protected void |
initParameters()
Initializes object after configuration parameters are loaded.
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protected void |
readValues(boolean all)
Retrieves relavant parameters values from the DOM tree.
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java.lang.String |
toString()
Returns the XML configuration in a string.
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addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, fromFile, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDefaultStandardizerConfiguration, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfMetrics, getNumberOfWeights, getScaleFactor, getScalingHypothesis, getScreeningConfigurationString, getThreshold, getThreshold, getTverskyAlpha, getTverskyBeta, getWeights, importNodes, isAsymmetric, isCellwiseWeights, isNormalized, isScaled, isStandardizationMandatory, isWeighted, processDocument, readFromXmlFile, readFromXmlString, readMetricParameters, readMetricWeights, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setCurrentParametrizedMetric, setLength, setNormalized, setOutputPrecision, setParameters, setParameters, setScaleFactor, setScalingHypothesis, setThreshold, setWeights, standardize, toString, writeMetricParameter
public BCUTParameters()
public BCUTParameters(java.io.File configFile) throws MDParametersException
configFile
- XML configuration fileMDParametersException
- missing or bad XML configurationpublic BCUTParameters(java.lang.String XMLconfig) throws MDParametersException
XMLconfig
- XML configuration stringMDParametersException
- missing or bad XML configurationpublic java.lang.String toString()
toString
in class MDParameters
public void fromString(java.lang.String parameterString) throws MDParametersException
fromString
in class MDParameters
parameterString
- parameters in stringMDParametersException
- when the parameter string is not well-formedpublic int getLowestEigenvaluesCount(int idx)
idx
- the index of descriptorpublic int getHighestEigenvaluesCount(int idx)
idx
- the index of descriptorpublic java.lang.String getType(int idx)
idx
- the index of descriptorpublic int getTypeCount()
public java.lang.String getDefaultDocumentFrame()
getDefaultDocumentFrame
in class MDParameters
protected void initParameters()
MDParameters
initParameters
in class MDParameters
protected java.lang.String[] generate(Molecule m, MolecularDescriptor bc) throws MDGeneratorException
MolecularDescriptor
object.m
- the Molecule
for which the descriptor is
generatedbc
- the BCUT descriptor will be stored here (out parameter)MDGeneratorException
protected int getNumberOfWeights(int parametrizedMetricIndex) throws java.lang.IllegalArgumentException
MolecularDescriptor
class or its derived classes, but not
to parametrized metric.getNumberOfWeights
in class MDParameters
parametrizedMetricIndex
- parametrized metric indexjava.lang.IllegalArgumentException
- if the given parameter is not a
valid metric indexprotected void readValues(boolean all) throws MDParametersException
readValues
in class MDParameters
all
- indicates if the entire document has to be processed
in which case the existing configuration is overwrittenMDParametersException