PeptideSearchEngineFIAlgorithm

class pyopenms.PeptideSearchEngineFIAlgorithm

Bases: object

Cython implementation of _PeptideSearchEngineFIAlgorithm

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’, ‘ProgressLogger’]

Fragment-index-based peptide database search algorithm (experimental).

Provides a self-contained search engine that matches MS/MS spectra against a protein database using an FI (Fragment Index). Typical usage: - Configure parameters via DefaultParamHandler (mass tolerances, enzyme, charges, etc.) - Call search() with an input mzML file and a FASTA database to populate identification

outputs (ProteinIdentification and PeptideIdentificationList)

• Intended for educational/prototyping use and to demonstrate FI-backed searching

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeptideSearchEngineFIAlgorithm) → None

Methods

__init__
endProgress(self)	Ends the progress display
getDefaults(self)	Returns the default parameters
getLogType(self)	Returns the type of progress log being used
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getSubsections(self)
nextProgress(self)	Increment progress by 1 (according to range begin-end)
search(self, in_mzML, in_db, prot_ids, pep_ids)	Search spectra in an mzML file against a protein database using an FI-backed workflow.
setLogType(self, in_0)	Sets the progress log that should be used.
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters
setProgress(self, value)	Sets the current progress
startProgress(self, begin, end, label)

PeptideSearchEngineFIAlgorithm_ExitCodes

alias of __PeptideSearchEngineFIAlgorithm_ExitCodes

endProgress(self) → None

Ends the progress display

getDefaults(self) → Param

Returns the default parameters

getLogType(self) → int

Returns the type of progress log being used

getName(self) → bytes | str | String

Returns the name

getParameters(self) → Param

Returns the parameters

getSubsections(self) → List[bytes]

nextProgress(self) → None

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

search(self, in_mzML: bytes | str | String, in_db: bytes | str | String, prot_ids: List[ProteinIdentification], pep_ids: PeptideIdentificationList) → int

Search spectra in an mzML file against a protein database using an FI-backed workflow.

Populates protein and peptide identifications, including search meta data, PSM hits, and search engine annotations. Parameters are taken from this instance.

Parameters:

• in_mzML – Input path to the mzML file containing MS/MS spectra to search

• in_db – Input path to the protein sequence database in FASTA format

• prot_ids – Output container receiving search meta data and protein-level information

• pep_ids – Output container receiving spectrum-level peptide identifications (PSMs)

Returns:

ExitCodes indicating success (EXECUTION_OK) or the encountered error condition

setLogType(self, in_0: int) → None

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

setName(self, in_0: bytes | str | String) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters

setProgress(self, value: int) → None

Sets the current progress

startProgress(self, begin: int, end: int, label: bytes | str | String) → None