chemaxon.descriptors.scalars
Class HBParameters

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

public class HBParameters
extends SDParameters

Manages parameters for the HDon and HAcc scalar descriptor classes. The native format of the parameter configuration is XML.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

static int

DEFAULT_PH default values for parameters

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

HBParameters()
Creates an empty object.

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

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

Method Summary

protected float	generate(Molecule m) Calculates the descriptor value for the given molecule.
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 relevant 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_PH

public static final int DEFAULT_PH

default values for parameters

See Also:

Constant Field Values

Constructor Detail

HBParameters

public HBParameters()

Creates an empty object. Initializes parameters to default values.

HBParameters

public HBParameters(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

HBParameters

public HBParameters(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

Calculates the descriptor value for the given molecule.

Parameters:

m - input molecule for which the descirptor is calculated

Returns:

the value of the descr

Throws:

MDGeneratorException

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Picks relevant 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