SiriusAdapterAlgorithm

class pyopenms.SiriusAdapterAlgorithm

Bases: object

Cython implementation of _SiriusAdapterAlgorithm

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SiriusAdapterAlgorithm.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void SiriusAdapterAlgorithm()

  • Cython signature: void SiriusAdapterAlgorithm(SiriusAdapterAlgorithm &)

Methods

__init__

  • Cython signature: void SiriusAdapterAlgorithm()

callSiriusQProcess

Cython signature: libcpp_vector[String] callSiriusQProcess(const String & tmp_ms_file, const String & tmp_out_dir, String & executable, const String & out_csifingerid, bool decoy_generation)

determineSiriusExecutable

Cython signature: String determineSiriusExecutable(String & executable)

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getFilterByNumMassTraces

Cython signature: unsigned int getFilterByNumMassTraces()

getIsotopePatternIterations

Cython signature: int getIsotopePatternIterations()

getName

Cython signature: String getName() Returns the name

getNumberOfCSIFingerIDCandidates

Cython signature: int getNumberOfCSIFingerIDCandidates()

getNumberOfSiriusCandidates

Cython signature: int getNumberOfSiriusCandidates()

getParameters

Cython signature: Param getParameters() Returns the parameters

getPrecursorMzTolerance

Cython signature: double getPrecursorMzTolerance()

getPrecursorRtTolerance

Cython signature: double getPrecursorRtTolerance()

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

isFeatureOnly

Cython signature: bool isFeatureOnly()

isNoMasstraceInfoIsotopePattern

Cython signature: bool isNoMasstraceInfoIsotopePattern()

logFeatureSpectraNumber

Cython signature: void logFeatureSpectraNumber(const String & featureinfo, FeatureMapping_FeatureToMs2Indices & feature_mapping, MSExperiment & spectra)

precursorMzToleranceUnitIsPPM

Cython signature: bool precursorMzToleranceUnitIsPPM()

preprocessingSirius

Cython signature: void preprocessingSirius(const String & featureinfo, MSExperiment & spectra, FeatureMapping_FeatureMappingInfo & fm_info, FeatureMapping_FeatureToMs2Indices & feature_mapping)

setName

Cython signature: void setName(const String &) Sets the name

setParameters

Cython signature: void setParameters(Param & param) Sets the parameters

sortSiriusWorkspacePathsByScanIndex

Cython signature: void sortSiriusWorkspacePathsByScanIndex(libcpp_vector[String] & subdirs)
callSiriusQProcess()

Cython signature: libcpp_vector[String] callSiriusQProcess(const String & tmp_ms_file, const String & tmp_out_dir, String & executable, const String & out_csifingerid, bool decoy_generation)

Parameters

  • tmp_ms_file – Path to temporary .ms file

  • tmp_out_dir – Path to temporary output folder

  • executable – Path to executable

  • out_csifingerid – Path to CSI:FingerID output (can be empty)

determineSiriusExecutable()

Cython signature: String determineSiriusExecutable(String & executable)

Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment —– :param executable: Path to the potential executable :returns: Path to SIRIUS executable

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getFilterByNumMassTraces()

Cython signature: unsigned int getFilterByNumMassTraces()

getIsotopePatternIterations()

Cython signature: int getIsotopePatternIterations()

getName()

Cython signature: String getName() Returns the name

getNumberOfCSIFingerIDCandidates()

Cython signature: int getNumberOfCSIFingerIDCandidates()

getNumberOfSiriusCandidates()

Cython signature: int getNumberOfSiriusCandidates()

getParameters()

Cython signature: Param getParameters() Returns the parameters

getPrecursorMzTolerance()

Cython signature: double getPrecursorMzTolerance()

getPrecursorRtTolerance()

Cython signature: double getPrecursorRtTolerance()

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

isFeatureOnly()

Cython signature: bool isFeatureOnly()

isNoMasstraceInfoIsotopePattern()

Cython signature: bool isNoMasstraceInfoIsotopePattern()

logFeatureSpectraNumber()

Cython signature: void logFeatureSpectraNumber(const String & featureinfo, FeatureMapping_FeatureToMs2Indices & feature_mapping, MSExperiment & spectra)

Parameters

  • featureinfo – Path to featureXML

  • feature_mapping – FeatureToMs2Indices with feature mapping

  • spectra – Input of MSExperiment with spectra information

precursorMzToleranceUnitIsPPM()

Cython signature: bool precursorMzToleranceUnitIsPPM()

preprocessingSirius()

Cython signature: void preprocessingSirius(const String & featureinfo, MSExperiment & spectra, FeatureMapping_FeatureMappingInfo & fm_info, FeatureMapping_FeatureToMs2Indices & feature_mapping)

Parameters

  • featureinfo – Path to featureXML

  • spectra – Input of MSExperiment with spectra information

  • fm_info – Emtpy - stores FeatureMaps and KDTreeMaps internally

  • feature_mapping – Empty FeatureToMs2Indices

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

sortSiriusWorkspacePathsByScanIndex()

Cython signature: void sortSiriusWorkspacePathsByScanIndex(libcpp_vector[String] & subdirs)