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