InspectInfile

class pyopenms.InspectInfile

Bases: object

Cython implementation of _InspectInfile

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Inspect input file adapter

Overload:

__init__(self, in_0: InspectInfile) → None

Methods

__init__	Overload:
getBlind(self)	Run inspect in a blind mode
getDb(self)	Specifies the name of a database (.trie file) to search
getEnzyme(self)	Specifies the name of a enzyme.
getInstrument(self)	If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass
getMaxPTMsize(self)	The maximum modification size (in Da) to consider in a blind search
getModifications
getModificationsPerPeptide(self)	Number of PTMs permitted in a single peptide
getMulticharge(self)	If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible
getPeakMassTolerance(self)	How far b and y peaks can be shifted from their expected masses.
getPrecursorMassTolerance(self)	Specifies the parent mass tolerance, in Daltons
getSpectra(self)	Specifies a spectrum file to search
getTagCount(self)	Number of tags to generate
handlePTMs(self, modification_line, ...)	Retrieves the name, mass change, affected residues, type and position for all modifications from a string
setBlind(self, blind)	Run inspect in a blind mode
setDb(self, db)	Specifies the name of a database (.trie file) to search
setEnzyme(self, enzyme)	Specifies the name of a enzyme.
setInstrument(self, instrument)	If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass
setMaxPTMsize(self, maxptmsize)	The maximum modification size (in Da) to consider in a blind search
setModificationsPerPeptide(self, ...)	Number of PTMs permitted in a single peptide
setMulticharge(self, multicharge)	If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible
setPeakMassTolerance(self, peak_mass_tolerance)	How far b and y peaks can be shifted from their expected masses
setPrecursorMassTolerance(self, ...)	Specifies the parent mass tolerance, in Daltons
setSpectra(self, spectra)	Specifies a spectrum file to search
setTagCount(self, TagCount)	Number of tags to generate
store(self, filename)	Stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution

getBlind(self) → int

Run inspect in a blind mode

getDb(self) → bytes | str | String

Specifies the name of a database (.trie file) to search

getEnzyme(self) → bytes | str | String

Specifies the name of a enzyme. “Trypsin”, “None”, and “Chymotrypsin” are the available values

getInstrument(self) → bytes | str | String

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass

getMaxPTMsize(self) → float

The maximum modification size (in Da) to consider in a blind search

getModifications()

getModificationsPerPeptide(self) → int

Number of PTMs permitted in a single peptide

getMulticharge(self) → int

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible

getPeakMassTolerance(self) → float

How far b and y peaks can be shifted from their expected masses.

getPrecursorMassTolerance(self) → float

Specifies the parent mass tolerance, in Daltons

getSpectra(self) → bytes | str | String

Specifies a spectrum file to search

getTagCount(self) → int

Number of tags to generate

handlePTMs(self, modification_line: bytes | str | String, modifications_filename: bytes | str | String, monoisotopic: bool) → None

Retrieves the name, mass change, affected residues, type and position for all modifications from a string

Parameters:

• modification_line –

• modifications_filename –

• monoisotopic – if true, masses are considered to be monoisotopic

Raises:

Exception: FileNotReadable if the modifications_filename could not be read

Raises:

Exception: FileNotFound if modifications_filename could not be found

Raises:

Exception: ParseError if modifications_filename could not be parsed

setBlind(self, blind: int) → None

Run inspect in a blind mode

setDb(self, db: bytes | str | String) → None

Specifies the name of a database (.trie file) to search

setEnzyme(self, enzyme: bytes | str | String) → None

Specifies the name of a enzyme. “Trypsin”, “None”, and “Chymotrypsin” are the available values

setInstrument(self, instrument: bytes | str | String) → None

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass

setMaxPTMsize(self, maxptmsize: float) → None

The maximum modification size (in Da) to consider in a blind search

setModificationsPerPeptide(self, modifications_per_peptide: int) → None

Number of PTMs permitted in a single peptide

setMulticharge(self, multicharge: int) → None

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible

setPeakMassTolerance(self, peak_mass_tolerance: float) → None

How far b and y peaks can be shifted from their expected masses

setPrecursorMassTolerance(self, precursor_mass_tolerance: float) → None

Specifies the parent mass tolerance, in Daltons

setSpectra(self, spectra: bytes | str | String) → None

Specifies a spectrum file to search

setTagCount(self, TagCount: int) → None

Number of tags to generate

store(self, filename: bytes | str | String) → None

Stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution