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