Package chemaxon.descriptors
Class BCUTParameters
- java.lang.Object
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- chemaxon.descriptors.MDParameters
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- chemaxon.descriptors.BCUTParameters
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@PublicAPI public class BCUTParameters extends MDParameters
Manages parameters for theBCUT
descriptor class. The native format of the parameter configuration is XML.- Since:
- JChem 2.3
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Field Summary
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Fields inherited from class chemaxon.descriptors.MDParameters
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
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Constructor Summary
Constructors Constructor Description BCUTParameters()
Creates an empty object.BCUTParameters(File configFile)
Creates a new object based on a given configuration file.BCUTParameters(String XMLconfig)
Creates a new object based on a given configuration string.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
fromString(String parameterString)
Sets parameters from a string representation.protected String[]
generate(Molecule m, MolecularDescriptor bc)
Calls the descriptor generator for the molecule provided and stores result (the descriptor) in theMolecularDescriptor
object.String
getDefaultDocumentFrame()
Gets the default XML configuration string.int
getHighestEigenvaluesCount(int idx)
Gets the number of highest eigenvalues calculated.int
getLowestEigenvaluesCount(int idx)
Gets the number of lowest eigenvalues calculated.protected int
getNumberOfWeights(int parametrizedMetricIndex)
Gets the number of weight factors used by the specified metric.String
getType(int idx)
Gets the type of the BCUT descriptor.int
getTypeCount()
Gets the count of descriptor types.protected void
initParameters()
Initializes object after configuration parameters are loaded.protected void
readValues(boolean all)
Retrieves relavant parameters values from the DOM tree.String
toString()
Returns the XML configuration in a string.-
Methods inherited from class chemaxon.descriptors.MDParameters
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
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Constructor Detail
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BCUTParameters
public BCUTParameters()
Creates an empty object. Initializes parameters to default values.
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BCUTParameters
public BCUTParameters(File configFile) throws MDParametersException
Creates a new object based on a given configuration file.- Parameters:
configFile
- XML configuration file- Throws:
MDParametersException
- missing or bad XML configuration
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BCUTParameters
public BCUTParameters(String XMLconfig) throws MDParametersException
Creates a new object based on a given configuration string.- Parameters:
XMLconfig
- XML configuration string- Throws:
MDParametersException
- missing or bad XML configuration
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Method Detail
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toString
public String toString()
Returns the XML configuration in a string.- Overrides:
toString
in classMDParameters
- Returns:
- configuration string in XML format
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fromString
public void fromString(String parameterString) throws MDParametersException
Sets parameters from a string representation. This method processes an XML format, but derived classes may overload this and define their own format.- Overrides:
fromString
in classMDParameters
- Parameters:
parameterString
- parameters in string- Throws:
MDParametersException
- when the parameter string is not well-formed
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getLowestEigenvaluesCount
public int getLowestEigenvaluesCount(int idx)
Gets the number of lowest eigenvalues calculated.- Parameters:
idx
- the index of descriptor- Returns:
- number of lowest eigenvalues
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getHighestEigenvaluesCount
public int getHighestEigenvaluesCount(int idx)
Gets the number of highest eigenvalues calculated.- Parameters:
idx
- the index of descriptor- Returns:
- number of highest eigenvalues
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getType
public String getType(int idx)
Gets the type of the BCUT descriptor. Valid types are: Burden, Charge, Polarizability, HBond.- Parameters:
idx
- the index of descriptor- Returns:
- type of the BCUT descriptor
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getTypeCount
public int getTypeCount()
Gets the count of descriptor types.- Returns:
- the count of descriptor types
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getDefaultDocumentFrame
public String getDefaultDocumentFrame()
Gets the default XML configuration string. This is needed when the XML configuration is not specified.- Overrides:
getDefaultDocumentFrame
in classMDParameters
- Returns:
- default XML configuration string of the BCUTParameters class
- Since:
- JChem 2.3
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initParameters
protected void initParameters()
Description copied from class:MDParameters
Initializes object after configuration parameters are loaded.- Overrides:
initParameters
in classMDParameters
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generate
protected String[] generate(Molecule m, MolecularDescriptor bc) throws MDGeneratorException
Calls the descriptor generator for the molecule provided and stores result (the descriptor) in theMolecularDescriptor
object.- Parameters:
m
- theMolecule
for which the descriptor is generatedbc
- the BCUT descriptor will be stored here (out parameter)- Returns:
- always null
- Throws:
MDGeneratorException
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getNumberOfWeights
protected int getNumberOfWeights(int parametrizedMetricIndex) throws IllegalArgumentException
Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by theMolecularDescriptor
class or its derived classes, but not to parametrized metric.- Overrides:
getNumberOfWeights
in classMDParameters
- Parameters:
parametrizedMetricIndex
- parametrized metric index- Returns:
- number of weights the metric uses
- Throws:
IllegalArgumentException
- if the given parameter is not a valid metric index
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readValues
protected void readValues(boolean all) throws MDParametersException
Retrieves relavant parameters values from the DOM tree.- Overrides:
readValues
in classMDParameters
- Parameters:
all
- indicates if the entire document has to be processed in which case the existing configuration is overwritten- Throws:
MDParametersException
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