InspectInfile#

class pyopenms.InspectInfile#

Bases: object

Cython implementation of _InspectInfile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1InspectInfile.html

__init__()#

Cython signature: void InspectInfile() Inspect input file adapter
Cython signature: void InspectInfile(InspectInfile &)

Methods

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

getBlind()#: Cython signature: unsigned int getBlind() Run inspect in a blind mode

getDb()#: Cython signature: String getDb() Specifies the name of a database (.trie file) to search

getEnzyme()#: Cython signature: String getEnzyme() Specifies the name of a enzyme. “Trypsin”, “None”, and “Chymotrypsin” are the available values

getInstrument()#: Cython signature: String getInstrument() If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass

getMaxPTMsize()#: Cython signature: float getMaxPTMsize() The maximum modification size (in Da) to consider in a blind search

getModifications()#

getModificationsPerPeptide()#: Cython signature: int getModificationsPerPeptide() Number of PTMs permitted in a single peptide

getMulticharge()#: Cython signature: unsigned int getMulticharge() If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible

getPeakMassTolerance()#: Cython signature: float getPeakMassTolerance() How far b and y peaks can be shifted from their expected masses.

getPrecursorMassTolerance()#: Cython signature: float getPrecursorMassTolerance() Specifies the parent mass tolerance, in Daltons

getSpectra()#: Cython signature: String getSpectra() Specifies a spectrum file to search

getTagCount()#: Cython signature: int getTagCount() Number of tags to generate

handlePTMs()#

Cython signature: void handlePTMs(const String & modification_line, const String & modifications_filename, bool monoisotopic)

:param modification_line :param modifications_filename :param 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()#: Cython signature: void setBlind(unsigned int blind) Run inspect in a blind mode

setDb()#: Cython signature: void setDb(const String & db) Specifies the name of a database (.trie file) to search

setEnzyme()#: Cython signature: void setEnzyme(const String & enzyme) Specifies the name of a enzyme. “Trypsin”, “None”, and “Chymotrypsin” are the available values

setInstrument()#: Cython signature: void setInstrument(const String & instrument) If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass

setMaxPTMsize()#: Cython signature: void setMaxPTMsize(float maxptmsize) The maximum modification size (in Da) to consider in a blind search

setModificationsPerPeptide()#: Cython signature: void setModificationsPerPeptide(int modifications_per_peptide) Number of PTMs permitted in a single peptide

setMulticharge()#: Cython signature: void setMulticharge(unsigned int multicharge) If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible

setPeakMassTolerance()#: Cython signature: void setPeakMassTolerance(float peak_mass_tolerance) How far b and y peaks can be shifted from their expected masses

setPrecursorMassTolerance()#: Cython signature: void setPrecursorMassTolerance(float precursor_mass_tolerance) Specifies the parent mass tolerance, in Daltons

setSpectra()#: Cython signature: void setSpectra(const String & spectra) Specifies a spectrum file to search

setTagCount()#: Cython signature: void setTagCount(int TagCount) Number of tags to generate

store()#: Cython signature: void store(const String & filename) Stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution