PrecursorIonSelectionPreprocessing#

class pyopenms.PrecursorIonSelectionPreprocessing#

Bases: object

Cython implementation of _PrecursorIonSelectionPreprocessing

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PrecursorIonSelectionPreprocessing) → None

Methods

`__init__`	Overload:
`dbPreprocessing`	Overload:
`getDefaults`(self)	Returns the default parameters
`getGaussMu`(self)	Returns the Gauss Mu value
`getGaussSigma`(self)	Returns the Gauss Sigma value
`getMasses`(self, acc)
`getName`(self)	Returns the name
`getPT`(self, prot_id, peptide_index)	Returns the PT value
`getParameters`(self)	Returns the parameters
`getRT`(self, prot_id, peptide_index)	Returns the RT value
`getRTProbability`	Overload:
`getSubsections`(self)
`getWeight`(self, mass)	Returns the weighted frequency of a mass
`loadPreprocessing`(self)	Loads tryptic peptide masses of a given database
`setFixedModifications`(self, modifications)
`setGaussianParameters`(self, mu, sigma)
`setName`(self, in_0)	Sets the name
`setParameters`(self, param)	Sets the parameters

dbPreprocessing()#

Overload:

dbPreprocessing(self, db_path: bytes | str | String, save: bool) → None

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences

Parameters:

db_path – Path to database file (fasta)
save – Flag if preprocessing should be stored

Raises:

Exception: FileNotFound is thrown if the file could not be found

Raises:

Exception: UnableToCreateFile if preprocessing file can’t be written

Overload:

dbPreprocessing(self, db_path: bytes | str | String, rt_model_path: bytes | str | String, dt_model_path: bytes | str | String, save: bool) → None

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences

Parameters:

db_path – Path to database file (fasta)
rt_model_path – Path to the retention time model
dt_model_path – Path to the detectability model
save – Flag if preprocessing should be stored

Raises:

Exception: FileNotFound is thrown if the file could not be found

Raises:

Exception: UnableToCreateFile if preprocessing file can’t be written

getDefaults(self) → Param#: Returns the default parameters

getGaussMu(self) → float#: Returns the Gauss Mu value

getGaussSigma(self) → float#: Returns the Gauss Sigma value

getMasses(self, acc: bytes | str | String) → List[float]#

getName(self) → bytes | str | String#: Returns the name

getPT(self, prot_id: bytes | str | String, peptide_index: int) → float#: Returns the PT value

getParameters(self) → Param#: Returns the parameters

getRT(self, prot_id: bytes | str | String, peptide_index: int) → float#: Returns the RT value

getRTProbability()#

Overload:

getRTProbability(self, prot_id: bytes | str | String, peptide_index: int, feature: Feature) → float

Overload:

getRTProbability(self, pred_rt: float, feature: Feature) → float

getSubsections(self) → List[bytes]#

getWeight(self, mass: float) → float#: Returns the weighted frequency of a mass

loadPreprocessing(self) → None#: Loads tryptic peptide masses of a given database

setFixedModifications(self, modifications: List[bytes]) → None#

setGaussianParameters(self, mu: float, sigma: float) → None#

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

setParameters(self, param: Param) → None#: Sets the parameters