MRMDecoy

class pyopenms.MRMDecoy

Bases: DefaultParamHandler

This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object

__init__() → None

__init__(arg: pyopenms.MRMDecoy, /) → None

Methods

__init__()
endProgress([bytes_processed])	Ends the progress display
findFixedResidues(sequence, keepN, keepC, ...)	Find all residues in a sequence that should not be reversed / shuffled
generateDecoys(exp, method, ...[, ...])	Generate decoys from a TargetedExperiment (shuffle_seed=-1 uses time-based seeding)
getDefaults()	Returns the default parameters
getLogType()	Returns the type of progress log being used
getName()	Returns the name
getParameters()	Returns the parameters
getSubsections()
nextProgress()	Increment progress by 1 (according to range begin-end)
setLogType(type)	Sets the progress log that should be used.
setName(name)	Sets the name
setParameters(param)	Sets the parameters
setProgress(value)	Sets the current progress
startProgress(begin, end, label)

endProgress(bytes_processed: int = 0) → None

Ends the progress display

static findFixedResidues(sequence: str, keepN: bool, keepC: bool, keep_const_pattern: str) → list[int]

Find all residues in a sequence that should not be reversed / shuffled

Parameters:

• sequence – The amino acid sequence

• keepN – Whether to keep N terminus constant

• keepC – Whether to keep C terminus constant

• keep_const_pattern – A string containing the AA to not change (e.g. ‘KRP’)

generateDecoys(exp: pyopenms.TargetedExperiment, method: str, aim_decoy_fraction: float, switchKR: bool, decoy_tag: str, max_attempts: int, identity_threshold: float, precursor_mz_shift: float, product_mz_shift: float, product_mz_threshold: float, fragment_types: list[str], fragment_charges: collections.abc.Sequence[int], enable_specific_losses: bool, enable_unspecific_losses: bool, round_decPow: int = -4, shuffle_seed: int = 1) → pyopenms.TargetedExperiment

Generate decoys from a TargetedExperiment (shuffle_seed=-1 uses time-based seeding)

getDefaults() → pyopenms.Param

Returns the default parameters

getLogType() → pyopenms.ProgressLogger.LogType

Returns the type of progress log being used

getName() → str

Returns the name

getParameters() → pyopenms.Param

Returns the parameters

getSubsections() → list[str]

nextProgress() → None

Increment progress by 1 (according to range begin-end)

setLogType(type: pyopenms.ProgressLogger.LogType) → None

Sets the progress log that should be used. The default type is NONE!

setName(name: str) → None

Sets the name

setParameters(param: pyopenms.Param) → None

Sets the parameters

setProgress(value: int) → None

Sets the current progress

startProgress(begin: int, end: int, label: str) → None