chemaxon.descriptors

Class RFParameters

java.lang.Object

chemaxon.descriptors.MDParameters

chemaxon.descriptors.RFParameters

@PublicAPI
public class RFParameters
extends MDParameters

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

Since:

JChem 3.2

Version:

5.1.2 09/24/2008

Author:

Zsolt Mohacsi

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BITS_SET
static int	DEFAULT_BOND_COUNT
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, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights

Constructor Summary

Constructors

Constructor and Description
RFParameters() Creates an empty object.
RFParameters(java.io.File configFile) Creates a new object based on a given configuration file.
RFParameters(java.lang.String XMLconfig) Creates a new object based on a given configuration string.

Method Summary

Modifier and Type	Method and Description
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 md) Calls RFGenerator and generates the descriptor for the given molecule.
int	getBitCount() Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.
int	getBondCount() Gets the preset path length (number of adjacent bonds) parameter.
java.lang.String	getDefaultDocumentFrame() Get the default XML configuration string.
boolean	getEnableStandardization() Shows if standardization should be applied of not.
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 reaction 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 ReactionFingerprint.
protected void	readValues(boolean all) Picks parameters values from the DOM tree.
void	setBitCount(int bitCount) Sets the bit count (number of fingerprint bits to be set to 1) parameter.
void	setBondCount(int bondCount) Sets the path length (number of adjacent bonds) parameter.
void	setEnableStandardization(boolean useStandardization) Sets if standardization is applied.
void	setLength(int length) Sets the length (number of bits) of the reaction fingerprint.

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

DEFAULT_LENGTH

public static final int DEFAULT_LENGTH

default values for parameters

See Also:

Constant Field Values

DEFAULT_BOND_COUNT

public static final int DEFAULT_BOND_COUNT

See Also:

Constant Field Values

DEFAULT_BITS_SET

public static final int DEFAULT_BITS_SET

See Also:

Constant Field Values

Constructor Detail

RFParameters

public RFParameters()

Creates an empty object. Initializes parameters to default values.

RFParameters

public RFParameters(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

RFParameters

public RFParameters(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

Sets the length (number of bits) of the reaction fingerprint.

Overrides:

setLength in class MDParameters

Parameters:

length - number of bits

Throws:

MDParametersException - if argument is not multiple of 32

setBondCount

public void setBondCount(int bondCount)

Sets the path length (number of adjacent bonds) parameter.

Parameters:

bondCount - the bond count parameter

setBitCount

public void setBitCount(int bitCount)

Sets the bit count (number of fingerprint bits to be set to 1) parameter.

Parameters:

bitCount - the bit count parameter

initGenerator

protected void initGenerator()
                      throws MDParametersException

Initializes the reaction fingerprint generator.

Throws:

MDParametersException

init

protected void init()

This method is called by the constructors before processing the XML configuration. It creates a ReactionFingerprint 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 md)
                               throws MDGeneratorException

Calls RFGenerator and generates the descriptor for the given molecule.

Parameters:

m - a molecular structure

md - the molecular 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

getBondCount

public int getBondCount()

Gets the preset path length (number of adjacent bonds) parameter.

Returns:

the bond count parameter

getBitCount

public int getBitCount()

Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.

Returns:

the bit count parameter

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 ReactionFingerprint XML configuration is not specified.

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the RFParameters class

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Processes pars of the XML configuration specific to ReactionFingerprint. 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 parameters 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

setEnableStandardization

public void setEnableStandardization(boolean useStandardization)

Sets if standardization is applied. As default it is. Disable it in case the standardization/aromatization is already done beforehand.

Parameters:

useStandardization -

getEnableStandardization

public boolean getEnableStandardization()

Shows if standardization should be applied of not. See setEnableStandardization(boolean).

Returns: