SiriusAdapterAlgorithm#

class pyopenms.SiriusAdapterAlgorithm#

Bases: object

Cython implementation of _SiriusAdapterAlgorithm

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: SiriusAdapterAlgorithm) → None

Methods

__init__

Overload:

callSiriusQProcess(self, tmp_ms_file, ...)

Call SIRIUS with QProcess

determineSiriusExecutable(self, executable)

Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment

getDefaults(self)

Returns the default parameters

getFilterByNumMassTraces(self)

getIsotopePatternIterations(self)

getName(self)

Returns the name

getNumberOfSiriusCandidates(self)

getParameters(self)

Returns the parameters

getPrecursorMzTolerance(self)

getPrecursorRtTolerance(self)

getSubsections(self)

isFeatureOnly(self)

isNoMasstraceInfoIsotopePattern(self)

logFeatureSpectraNumber(self, featureinfo, ...)

Logs number of features and spectra used

logInSiriusAccount(self, executable, email, ...)

Log in to SIRIUS using your personal account

precursorMzToleranceUnitIsPPM(self)

preprocessingSirius(self, featureinfo, ...)

Preprocessing needed for SIRIUS

setName(self, in_0)

Sets the name

setParameters(self, param)

Sets the parameters

sortSiriusWorkspacePathsByScanIndex

__static_SiriusAdapterAlgorithm_sortSiriusWorkspacePathsByScanIndex(subdirs: List[bytes] ) -> None
callSiriusQProcess(self, tmp_ms_file: bytes | str | String, tmp_out_dir: bytes | str | String, executable: String, out_csifingerid: bytes | str | String, decoy_generation: bool) → List[bytes]#

Call SIRIUS with QProcess

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(self, executable: String) → bytes | str | String#

Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment

Parameters:

executable – Path to the potential executable

Returns:

Path to SIRIUS executable

getDefaults(self) → Param#

Returns the default parameters

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

Returns the name

getNumberOfSiriusCandidates(self) → int#
getParameters(self) → Param#

Returns the parameters

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

Logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters:

  • featureinfo – Path to featureXML

  • feature_mapping – FeatureToMs2Indices with feature mapping

  • spectra – Input of MSExperiment with spectra information

logInSiriusAccount(self, executable: String, email: bytes | str | String, password: bytes | str | String) → None#

Log in to SIRIUS using your personal account

Parameters:

  • executable – Path to executable.

  • email – User account E-Mail.

  • password – User account password.

precursorMzToleranceUnitIsPPM(self) → bool#
preprocessingSirius(self, featureinfo: bytes | str | String, spectra: MSExperiment, fm_info: FeatureMapping_FeatureMappingInfo, feature_mapping: FeatureMapping_FeatureToMs2Indices) → None#

Preprocessing needed for SIRIUS

Filter number of masstraces and perform 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(self, in_0: bytes | str | String) → None#

Sets the name

setParameters(self, param: Param) → None#

Sets the parameters

sortSiriusWorkspacePathsByScanIndex()#

__static_SiriusAdapterAlgorithm_sortSiriusWorkspacePathsByScanIndex(subdirs: List[bytes] ) -> None