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