Package chemaxon.descriptors

Class CDParameters

java.lang.Object

chemaxon.descriptors.MDParameters

chemaxon.descriptors.CDParameters

@PublicAPI
public class CDParameters
extends MDParameters

Manages parameters the CustomDescriptor class.

Since:

JChem 2.3

Field Summary

Fields

Modifier and Type	Field	Description
static int	BINARY_DESCRIPTOR	descriptor type constants
protected int	descrType	descriptor type
static int	FLOAT_DESCRIPTOR
static int	INTEGER_DESCRIPTOR
protected org.dom4j.Element	parameters	node in the DOM tree built from the XML configuration

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, generator, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights

Constructor Summary

Constructors

Constructor	Description
CDParameters()	Creates an empty object.
CDParameters(int type)	Creates an empty object of the given type.
CDParameters(File configFile)	Creates a new descriptor configured from the given file.
CDParameters(String XMLconfig)	Creates a new object based on a given configuration string.

Method Summary

Modifier and Type	Method	Description
void	fromFile(File parameterFile)	Sets parameters from an XML file.
void	fromString(String parameterString)	Sets parameters from a string representation.
String	getDefaultDocumentFrame()	Gets the XML configuration string.
int	getDescrType()	Gets the type of the descriptor.
protected int	getNumberOfWeights(int parametrizedMetricIndex)	Gets the number of weight factors used by the specified metric.
protected void	init()	This method is called by the constructors before processing the XML configuration.
protected void	initGenerator()	This method is void in this class as custom descriptors are opaque, their internal structure is not known.
protected void	initParameters()	Initializes data members that depend on the XML configuration but are not directly taken from it.
protected void	processDocument(boolean all)	Processes parts of the XML configuration that are specific to CustomDescriptor.
protected void	readValues(boolean all)	Picks parameter values from the DOM tree.
void	setLength(int length)	Sets the length (number of cells) of the descriptor.

Methods inherited from class chemaxon.descriptors.MDParameters

addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, 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, readFromXmlFile, readFromXmlString, readMetricParameters, readMetricWeights, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setCurrentParametrizedMetric, setNormalized, setOutputPrecision, setParameters, setParameters, setScaleFactor, setScalingHypothesis, setThreshold, setWeights, standardize, toString, toString, writeMetricParameter

Methods inherited from class java.lang.Object

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

Field Detail

BINARY_DESCRIPTOR

public static final int BINARY_DESCRIPTOR

descriptor type constants

See Also:

Constant Field Values

INTEGER_DESCRIPTOR

public static final int INTEGER_DESCRIPTOR

See Also:

Constant Field Values

FLOAT_DESCRIPTOR

public static final int FLOAT_DESCRIPTOR

See Also:

Constant Field Values

descrType

protected int descrType

descriptor type

parameters

protected org.dom4j.Element parameters

node in the DOM tree built from the XML configuration

Constructor Detail

CDParameters

public CDParameters()

Creates an empty object. The type of the descriptor is not yet determined.

CDParameters

public CDParameters(int type)

Creates an empty object of the given type. Initializes to default values.

CDParameters

public CDParameters(File configFile)
             throws MDParametersException

Creates a new descriptor configured from the given file.

Parameters:

configFile - XML configuration file

Throws:

MDParametersException - missing or bad XML configuration

CDParameters

public CDParameters(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

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 class MDParameters

Parameters:

parameterString - parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

fromFile

public void fromFile(File parameterFile)
              throws MDParametersException

Sets parameters from an XML file. Derived classes may overload this and define their own format (even other than XML).

Overrides:

fromFile in class MDParameters

Parameters:

parameterFile - initialized parameter file

Throws:

MDParametersException - failed to process parameter file

setLength

public void setLength(int length)
               throws MDParametersException

Description copied from class: MDParameters

Sets the length (number of cells) of the descriptor.

Overrides:

setLength in class MDParameters

Parameters:

length - the required length (cell count)

Throws:

MDParametersException - if argument is not positive

initGenerator

protected void initGenerator()
                      throws MDParametersException

This method is void in this class as custom descriptors are opaque, their internal structure is not known. Derived classes that implement user defined or 3rd party descriptors should overload this function and provide the procedure for descriptor generation.

Throws:

MDParametersException

init

protected void init()

This method is called by the constructors before processing the XML configuration. It creates a CustomDescriptor object defined in MDParameters.md. Metircs defined by the descirptor class are retrieved through this object.

initParameters

protected void initParameters()

Initializes data members that depend on the XML configuration but are not directly taken from it.

Overrides:

initParameters in class MDParameters

getDescrType

public int getDescrType()

Gets the type of the descriptor.

Returns:

type of the descriptor (BINARY_DESCRIPTOR, INTEGER_DESCRIPTOR or FLOAT_DESCRIPTOR)

getNumberOfWeights

protected int getNumberOfWeights(int parametrizedMetricIndex)
                          throws IllegalArgumentException

Gets the number of weight factors used by the specified metric. T

Overrides:

getNumberOfWeights in class MDParameters

Parameters:

parametrizedMetricIndex - parametrized metric index

Returns:

number of weights the metric uses

Throws:

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

getDefaultDocumentFrame

public String getDefaultDocumentFrame()

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

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the CDParameters class

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Processes parts of the XML configuration that are specific to CustomDescriptor. Find the node in the DOM tree and leaves the rest of the work to the parent class.

Overrides:

processDocument in class MDParameters

Parameters:

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

Throws:

MDParametersException

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Picks parameter 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