chemaxon.descriptors.scalars
Class LDParameters

java.lang.Object
  chemaxon.descriptors.MDParameters
      chemaxon.descriptors.SDParameters
          chemaxon.descriptors.scalars.LDParameters

public class LDParameters
extends SDParameters

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

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

static int	DEFAULT_LOWER_BOUND default values for parameters
static int	DEFAULT_PH
static int	DEFAULT_STEP_SIZE
static int	DEFAULT_UPPER_BOUND

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

LDParameters()
Creates an empty object.

LDParameters(java.io.File configFile)
Creates a new object based on a given configuration file.

LDParameters(java.lang.String XMLconfig)
Creates a new object based on a given configuration string.

Method Summary

protected float	generate(Molecule m)
protected void	initParameters() Initializes those data members that depend on the XML configuration but are not directly taken from it.
protected void	readValues(boolean all) Picks parameters values from the DOM tree.
java.lang.String	toString() Returns the XML configuration in a string.

Methods inherited from class chemaxon.descriptors.SDParameters

fromFile, fromString, getNumberOfMetrics, getType, init, processDocument, setLength

Methods inherited from class chemaxon.descriptors.MDParameters

addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDefaultDocumentFrame, getDefaultStandardizerConfiguration, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfWeights, 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, writeMetricParameter

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_LOWER_BOUND

public static final int DEFAULT_LOWER_BOUND

default values for parameters

See Also:

Constant Field Values

DEFAULT_UPPER_BOUND

public static final int DEFAULT_UPPER_BOUND

See Also:

Constant Field Values

DEFAULT_STEP_SIZE

public static final int DEFAULT_STEP_SIZE

See Also:

Constant Field Values

DEFAULT_PH

public static final int DEFAULT_PH

See Also:

Constant Field Values

Constructor Detail

LDParameters

public LDParameters()

Creates an empty object. Initializes parameters to default values.

LDParameters

public LDParameters(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

LDParameters

public LDParameters(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

initParameters

protected void initParameters()

Description copied from class: SDParameters

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

Overrides:

initParameters in class SDParameters

generate

protected float generate(Molecule m)
                  throws MDGeneratorException

Throws:

MDGeneratorException

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Picks parameters values from the DOM tree.

Overrides:

readValues in class SDParameters

Parameters:

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

Throws:

MDParametersException