chemaxon.descriptors

Class BCUTParameters

java.lang.Object

chemaxon.descriptors.MDParameters

chemaxon.descriptors.BCUTParameters

@PublicAPI
public class BCUTParameters
extends MDParameters

Manages parameters for the BCUT descriptor class. The native format of the parameter configuration is XML.

Since:

JChem 2.3

Author:

Miklos Vargyas

Field Summary

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

Constructor Summary

Constructors

Constructor and Description
BCUTParameters() Creates an empty object.
BCUTParameters(java.io.File configFile) Creates a new object based on a given configuration file.
BCUTParameters(java.lang.String XMLconfig) Creates a new object based on a given configuration string.

Method Summary

Modifier and Type	Method and Description
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
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.
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.
java.lang.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.
java.lang.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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BCUTParameters

public BCUTParameters()

Creates an empty object. Initializes parameters to default values.

BCUTParameters

public BCUTParameters(java.io.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

BCUTParameters

public BCUTParameters(java.lang.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

Method Detail

toString

public java.lang.String toString()

Returns the XML configuration in a string.

Overrides:

toString in class MDParameters

Returns:

configuration string in XML format

fromString

public void fromString(java.lang.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 class MDParameters

Parameters:

parameterString - parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

getLowestEigenvaluesCount

public int getLowestEigenvaluesCount(int idx)

Gets the number of lowest eigenvalues calculated.

Parameters:

idx - the index of descriptor

Returns:

number of lowest eigenvalues

getHighestEigenvaluesCount

public int getHighestEigenvaluesCount(int idx)

Gets the number of highest eigenvalues calculated.

Parameters:

idx - the index of descriptor

Returns:

number of highest eigenvalues

getType

public java.lang.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

getTypeCount

public int getTypeCount()

Gets the count of descriptor types.

Returns:

the count of descriptor types

getDefaultDocumentFrame

public java.lang.String getDefaultDocumentFrame()

Gets the default XML configuration string. This is needed when the XML configuration is not specified.

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the BCUTParameters class

Since:

JChem 2.3

initParameters

protected void initParameters()

Description copied from class: MDParameters

Initializes object after configuration parameters are loaded.

Overrides:

initParameters in class MDParameters

generate

protected java.lang.String[] generate(Molecule m,
                                      MolecularDescriptor bc)
                               throws MDGeneratorException

Calls the descriptor generator for the molecule provided and stores result (the descriptor) in the MolecularDescriptor object.

Parameters:

m - the Molecule for which the descriptor is generated

bc - the BCUT descriptor will be stored here (out parameter)

Returns:

always null

Throws:

MDGeneratorException

getNumberOfWeights

protected int getNumberOfWeights(int parametrizedMetricIndex)
                          throws java.lang.IllegalArgumentException

Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by the MolecularDescriptor class or its derived classes, but not to parametrized metric.

Overrides:

getNumberOfWeights in class MDParameters

Parameters:

parametrizedMetricIndex - parametrized metric index

Returns:

number of weights the metric uses

Throws:

java.lang.IllegalArgumentException - if the given parameter is not a valid metric index

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Retrieves relavant parameters values from the DOM tree.

Overrides:

readValues in class MDParameters

Parameters:

all - indicates if the entire document has to be processed in which case the existing configuration is overwritten

Throws:

MDParametersException