DecoyGenerator

class pyopenms.DecoyGenerator

Bases: object

Cython implementation of _DecoyGenerator

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: DecoyGenerator) → None

Methods

__init__
reversePeptides(self, protein, protease)	Reverses the protein's peptide sequences between enzymatic cutting positions
reverseProtein(self, protein)	Reverses the protein sequence
setSeed(self, in_0)
shuffle(self, protein, protease, decoy_factor)	Generate decoy protein sequences using shuffle algorithm.
shufflePeptides(self, aas, protease, ...)	Shuffle the protein's peptide sequences between enzymatic cutting positions, each peptide is shuffled @param max_attempts times to minimize sequence identity

reversePeptides(self, protein: AASequence, protease: bytes | str | String) → AASequence

Reverses the protein’s peptide sequences between enzymatic cutting positions

reverseProtein(self, protein: AASequence) → AASequence

Reverses the protein sequence

setSeed(self, in_0: int) → None

shuffle(self, protein: AASequence, protease: bytes | str | String, decoy_factor: int) → List[AASequence]

Generate decoy protein sequences using shuffle algorithm. Digests protein using specified protease and shuffles each peptide. For top-down proteomics use “no cleavage”. decoy_factor is the number of complete decoy proteins to generate. Returns vector of AASequence

shufflePeptides(self, aas: AASequence, protease: bytes | str | String, max_attempts: int) → AASequence

Shuffle the protein’s peptide sequences between enzymatic cutting positions, each peptide is shuffled @param max_attempts times to minimize sequence identity