Package chemaxon.descriptors.scalars
Class HBParameters
java.lang.Object
chemaxon.descriptors.MDParameters
chemaxon.descriptors.SDParameters
chemaxon.descriptors.scalars.HBParameters
Manages parameters for the
HDon
and HAcc
scalar
descriptor classes.
The native format of the parameter configuration is XML.- Since:
- JChem 2.2
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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, generator, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights
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Constructor Summary
ConstructorDescriptionCreates an empty object.HBParameters
(File configFile) Creates a new object based on a given configuration file.HBParameters
(String XMLconfig) Creates a new object based on a given configuration string. -
Method Summary
Modifier and TypeMethodDescriptionprotected float
Calculates the descriptor value for the given molecule.protected void
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.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
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Field Details
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DEFAULT_PH
public static final int DEFAULT_PHdefault values for parameters- See Also:
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Constructor Details
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HBParameters
public HBParameters()Creates an empty object. Initializes parameters to default values. -
HBParameters
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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HBParameters
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 Details
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toString
Returns the XML configuration in a string.- Overrides:
toString
in classMDParameters
- Returns:
- configuration string in XML format
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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 classSDParameters
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generate
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
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readValues
Picks relevant parameters values from the DOM tree.- Overrides:
readValues
in classSDParameters
- 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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