chemaxon.descriptors
Class ECFPParameters

java.lang.Object
  chemaxon.descriptors.MDParameters
      chemaxon.descriptors.ECFPParameters

public class ECFPParameters
extends MDParameters

Manages ECFP fingerprint parameters. This class reads, stores and provides parameters for ECFP class. These parameters together are called the ECFP fingerprint configuration. The native format of such configuration is XML.

Since:

JChem 5.4

Author:

Peter Kovacs (pkovacs84)

Field Summary

static int	DEFAULT_DIAMETER
static int	DEFAULT_LENGTH 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

ECFPParameters()
Creates an empty object.

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

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

Method Summary

void	fromFile(java.io.File parameterFile) Sets parameters from an XML file.
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
protected java.lang.String[]	generate(Molecule m, MolecularDescriptor ecfp) Calls ECFPGenerator and generates the descriptor for the given molecule.
java.lang.String	getDefaultDocumentFrame() Get the default XML configuration string.
static java.lang.String	getDefaultStandardizerConfiguration() Gets the default configuration of the standardizer.
int	getDiameter() Gets the preset diameter parameter.
boolean	getKeepCounts() Gets the counts (multiplicity) parameter.
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() Initializes the fingerprint generator.
protected void	initParameters() Initializes those data members that depend on the XML configuration but are not directly taken from it.
protected void	processDocument(boolean all) Processes pars of the XML configuration specific to ECFP.
protected void	readValues(boolean all) Picks parameter values from the DOM tree.
void	setDiameter(int diameter) Sets the diameter parameter.
void	setKeepCounts(boolean keepCounts) Sets the counts (multiplicity) parameter.
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, 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

DEFAULT_LENGTH

public static final int DEFAULT_LENGTH

default values for parameters

See Also:

Constant Field Values

DEFAULT_DIAMETER

public static final int DEFAULT_DIAMETER

See Also:

Constant Field Values

Constructor Detail

ECFPParameters

public ECFPParameters()

Creates an empty object. Initializes fingerprint parameters to default values.

ECFPParameters

public ECFPParameters(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

ECFPParameters

public ECFPParameters(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

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

fromFile

public void fromFile(java.io.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

setDiameter

public void setDiameter(int diameter)

Sets the diameter parameter. It specifies the diameter of the circular neighborhood considered for each atom.

getDiameter

public int getDiameter()

Gets the preset diameter parameter. It specifies the diameter of the circular neighborhood considered for each atom.

Returns:

the diameter parameter

setKeepCounts

public void setKeepCounts(boolean keepCounts)

Sets the counts (multiplicity) parameter. It controls whether the generated identifiers are stored with occurrence counts or each identifier is kept only once independently of the number of the corresponding substructural features in the input molecule.

Parameters:

keepCounts - counts parameter

getKeepCounts

public boolean getKeepCounts()

Gets the counts (multiplicity) parameter. It controls whether the generated identifiers are stored with occurrence counts or each identifier is kept only once independently of the number of the corresponding substructural features in the input molecule.

Returns:

counts parameter

initGenerator

protected void initGenerator()
                      throws MDParametersException

Initializes the fingerprint generator.

Throws:

MDParametersException

init

protected void init()

This method is called by the constructors before processing the XML configuration. It creates a ECFP object stored in MDParameters.md.

initParameters

protected void initParameters()

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

Overrides:

initParameters in class MDParameters

generate

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

Calls ECFPGenerator and generates the descriptor for the given molecule.

Parameters:

m - a molecular structure

ecfp - the ECFP descriptor generated for the given molecule, an output parameter

Returns:

names of Molecule Property-s (SDfile tags) set by the generator

Throws:

MDGeneratorException - when failed to generate descriptor

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

getDefaultDocumentFrame

public java.lang.String getDefaultDocumentFrame()

Get the default XML configuration string. This is needed when the optional ECFP XML configuration is not specified.

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the ECFPParameters class

getDefaultStandardizerConfiguration

public static java.lang.String getDefaultStandardizerConfiguration()

Gets the default configuration of the standardizer. This method is called if no standardizer configuration is set in the parameters configuration. The default standardization for ECFP includes aromatization.

Returns:

standardizer configuration XML string

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Processes pars of the XML configuration specific to ECFP. 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