Package chemaxon.descriptors
Class RFParameters
- java.lang.Object
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- chemaxon.descriptors.MDParameters
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- chemaxon.descriptors.RFParameters
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@PublicAPI public class RFParameters extends MDParameters
Manages reaction fingerprint parameters. This class reads, stores and provides parameters forReactionFingerprint
class. These parameters together are called the reaction fingerprint configuration. The native format of such configuration is XML.- Since:
- JChem 3.2
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Field Summary
Fields Modifier and Type Field 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
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Constructor Summary
Constructors Constructor Description RFParameters()
Creates an empty object.RFParameters(File configFile)
Creates a new object based on a given configuration file.RFParameters(String XMLconfig)
Creates a new object based on a given configuration string.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
fromFile(File parameterFile)
Sets parameters from an XML file.void
fromString(String parameterString)
Sets parameters from a string representation.protected String[]
generate(Molecule m, MolecularDescriptor md)
CallsRFGenerator
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.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 toReactionFingerprint
.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
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Field Detail
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DEFAULT_LENGTH
public static final int DEFAULT_LENGTH
default values for parameters- See Also:
- Constant Field Values
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DEFAULT_BOND_COUNT
public static final int DEFAULT_BOND_COUNT
- See Also:
- Constant Field Values
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DEFAULT_BITS_SET
public static final int DEFAULT_BITS_SET
- See Also:
- Constant Field Values
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Constructor Detail
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RFParameters
public RFParameters()
Creates an empty object. Initializes parameters to default values.
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RFParameters
public RFParameters(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
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RFParameters
public RFParameters(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
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Method Detail
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fromString
public void fromString(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 classMDParameters
- Parameters:
parameterString
- parameters in string- Throws:
MDParametersException
- when the parameter string is not well-formed
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fromFile
public void fromFile(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 classMDParameters
- Parameters:
parameterFile
- initialized parameter file- Throws:
MDParametersException
- failed to process parameter file
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setLength
public void setLength(int length) throws MDParametersException
Sets the length (number of bits) of the reaction fingerprint.- Overrides:
setLength
in classMDParameters
- Parameters:
length
- number of bits- Throws:
MDParametersException
- if argument is not multiple of 32
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setBondCount
public void setBondCount(int bondCount)
Sets the path length (number of adjacent bonds) parameter.- Parameters:
bondCount
- the bond count parameter
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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
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initGenerator
protected void initGenerator() throws MDParametersException
Initializes the reaction fingerprint generator.- Throws:
MDParametersException
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init
protected void init()
This method is called by the constructors before processing the XML configuration. It creates aReactionFingerprint
object stored inMDParameters.md
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initParameters
protected void initParameters()
Initializes those data members that depend on the XML configuration but are not directly taken from it.- Overrides:
initParameters
in classMDParameters
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generate
protected String[] generate(Molecule m, MolecularDescriptor md) throws MDGeneratorException
CallsRFGenerator
and generates the descriptor for the given molecule.- Parameters:
m
- a molecular structuremd
- 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
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getBondCount
public int getBondCount()
Gets the preset path length (number of adjacent bonds) parameter.- Returns:
- the bond count parameter
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getBitCount
public int getBitCount()
Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.- Returns:
- the bit count parameter
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getNumberOfWeights
protected int getNumberOfWeights(int parametrizedMetricIndex) throws IllegalArgumentException
Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by theMolecularDescriptor
class or its derived classes, but not to parametrized metric.- Overrides:
getNumberOfWeights
in classMDParameters
- Parameters:
parametrizedMetricIndex
- parametrized metric index- Returns:
- number of weights the metric uses
- Throws:
IllegalArgumentException
- if the given parameter is not a valid metric index
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getDefaultDocumentFrame
public String getDefaultDocumentFrame()
Get the default XML configuration string. This is needed when the optional ReactionFingerprint XML configuration is not specified.- Overrides:
getDefaultDocumentFrame
in classMDParameters
- Returns:
- default XML configuration string of the RFParameters class
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processDocument
protected void processDocument(boolean all) throws MDParametersException
Processes pars of the XML configuration specific toReactionFingerprint
. Find thenode in the DOM tree and leaves the rest of the work to the parent class. - Overrides:
processDocument
in classMDParameters
- 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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readValues
protected void readValues(boolean all) throws MDParametersException
Picks parameters values from the DOM tree.- Overrides:
readValues
in classMDParameters
- 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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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
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getEnableStandardization
public boolean getEnableStandardization()
Shows if standardization should be applied of not. SeesetEnableStandardization(boolean)
.- Returns:
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