@PublicAPI public class ECFPParameters extends MDParameters
ECFP
class. These parameters together are
called the ECFP fingerprint configuration. The native format of such
configuration is XML.Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_DIAMETER |
static int |
DEFAULT_LENGTH
default values for parameters
|
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 and Description |
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ECFPParameters()
Creates an empty object.
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ECFPParameters(java.io.File configFile)
Creates a new object based on a given configuration file.
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ECFPParameters(java.lang.String XMLconfig)
Creates a new object based on a given configuration string.
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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 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.
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boolean |
getKeepCounts()
Gets the counts (multiplicity) parameter.
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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.
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protected void |
initGenerator()
Initializes the fingerprint generator.
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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.
|
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
public static final int DEFAULT_LENGTH
public static final int DEFAULT_DIAMETER
public ECFPParameters()
public ECFPParameters(java.io.File configFile) throws MDParametersException
configFile
- XML configuration fileMDParametersException
- missing or bad XML configurationpublic ECFPParameters(java.lang.String XMLconfig) throws MDParametersException
XMLconfig
- XML configuration stringMDParametersException
- missing or bad XML configurationpublic void fromString(java.lang.String parameterString) throws MDParametersException
fromString
in class MDParameters
parameterString
- parameters in stringMDParametersException
- when the parameter string is not well-formedpublic void fromFile(java.io.File parameterFile) throws MDParametersException
fromFile
in class MDParameters
parameterFile
- initialized parameter fileMDParametersException
- failed to process parameter filepublic void setLength(int length) throws MDParametersException
MDParameters
setLength
in class MDParameters
length
- the required length (cell count)MDParametersException
- if argument is not positivepublic void setDiameter(int diameter)
public int getDiameter()
public void setKeepCounts(boolean keepCounts)
keepCounts
- counts parameterpublic boolean getKeepCounts()
protected void initGenerator() throws MDParametersException
MDParametersException
protected void init()
ECFP
object stored in
MDParameters.md
.protected void initParameters()
initParameters
in class MDParameters
protected java.lang.String[] generate(Molecule m, MolecularDescriptor ecfp) throws MDGeneratorException
ECFPGenerator
and generates the descriptor for the
given molecule.m
- a molecular structureecfp
- the ECFP descriptor generated for the given molecule,
an output parameterMDGeneratorException
- when failed to generate descriptorprotected int getNumberOfWeights(int parametrizedMetricIndex) throws java.lang.IllegalArgumentException
MolecularDescriptor
class or its derived classes, but not
to parametrized metric.getNumberOfWeights
in class MDParameters
parametrizedMetricIndex
- parametrized metric indexjava.lang.IllegalArgumentException
- if the given parameter is not a
valid metric indexpublic java.lang.String getDefaultDocumentFrame()
getDefaultDocumentFrame
in class MDParameters
public static java.lang.String getDefaultStandardizerConfiguration()
ECFP
includes aromatization.protected void processDocument(boolean all) throws MDParametersException
ECFP
.
Find the processDocument
in class MDParameters
all
- indicates if the entire document has to be processed
in which case the existing configuration is overwrittenMDParametersException
protected void readValues(boolean all) throws MDParametersException
readValues
in class MDParameters
all
- indicates if the entire document has to be processed
in which case the existing configuration is overwrittenMDParametersException