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)