SiriusExportAlgorithm#

class pyopenms.SiriusExportAlgorithm#

Bases: object

Cython implementation of _SiriusExportAlgorithm

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: SiriusExportAlgorithm) → None

Methods

__init__

Overload:

getDefaults(self)

Returns the default parameters

getFilterByNumMassTraces(self)

getIsotopePatternIterations(self)

getName(self)

Returns the name

getParameters(self)

Returns the parameters

getPrecursorMzTolerance(self)

getPrecursorRtTolerance(self)

getSubsections(self)

isFeatureOnly(self)

isNoMasstraceInfoIsotopePattern(self)

logFeatureSpectraNumber(self, ...)

Logs number of features and spectra used

precursorMzToleranceUnitIsPPM(self)

preprocessing(self, featureXML_path, ...)

Preprocessing needed for SIRIUS

run(self, mzML_files, featureXML_files, ...)

Runs SiriusExport with mzML and featureXML (optional) files as input.

setName(self, in_0)

Sets the name

setParameters(self, param)

Sets the parameters
getDefaults(self) → Param#

Returns the default parameters

getFilterByNumMassTraces(self) → int#
getIsotopePatternIterations(self) → int#
getName(self) → bytes | str | String#

Returns the name

getParameters(self) → Param#

Returns the parameters

getPrecursorMzTolerance(self) → float#
getPrecursorRtTolerance(self) → float#
getSubsections(self) → List[bytes]#
isFeatureOnly(self) → bool#
isNoMasstraceInfoIsotopePattern(self) → bool#
logFeatureSpectraNumber(self, featureXML_path: bytes | str | String, feature_ms2_indices: FeatureMapping_FeatureToMs2Indices, spectra: MSExperiment) → None#

Logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters:

  • featureXML_path – Path to featureXML

  • feature_ms2_indices – FeatureToMs2Indices with feature mapping

  • spectra – Input of MSExperiment with spectra information

precursorMzToleranceUnitIsPPM(self) → bool#
preprocessing(self, featureXML_path: bytes | str | String, spectra: MSExperiment, feature_mapping_info: FeatureMapping_FeatureMappingInfo, feature_ms2_indices: FeatureMapping_FeatureToMs2Indices) → None#

Preprocessing needed for SIRIUS

Filter number of masstraces and perform feature mapping

Parameters:

  • featureXML_path – Path to featureXML

  • spectra – Input of MSExperiment with spectra information

  • feature_mapping_info – Emtpy - stores FeatureMaps and KDTreeMaps internally

  • feature_ms2_indices – Empty FeatureToMs2Indices

run(self, mzML_files: List[bytes], featureXML_files: List[bytes], out_ms: bytes | str | String, out_compoundinfo: bytes | str | String) → None#

Runs SiriusExport with mzML and featureXML (optional) files as input.

Generates a SIRIUS .ms file and compound info table (optional).

Parameters:

  • mzML_files – List with paths to mzML files

  • featureXML_files – List with paths to featureXML files

  • out_ms – Output file name for SIRIUS .ms file

  • out_compoundinfo – Output file name for tsv file with compound info

setName(self, in_0: bytes | str | String) → None#

Sets the name

setParameters(self, param: Param) → None#

Sets the parameters