SequestInfile

class pyopenms.SequestInfile

Bases: object

Cython implementation of _SequestInfile

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Sequest input file adapter

Overload:

__init__(self, in_0: SequestInfile) → None

Methods

`__init__`	Overload:
`addEnzymeInfo`(self, enzyme_info)	Adds an enzyme to the list and sets is as used
`getDatabase`(self)	Returns the used database
`getEnzymeInfoAsString`(self)	Returns the enzyme list as a string
`getEnzymeName`(self)	Returns the enzyme used for cleavage
`getEnzymeNumber`(self)	Returns the enzyme used for cleavage (by means of the number from a list of enzymes)
`getIonCutoffPercentage`(self)	Returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks
`getIonSeriesWeights`(self)	Returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
`getMassTypeFragment`(self)	Returns the mass type of the fragments (0 - monoisotopic, 1 - average mass)
`getMassTypeParent`(self)	Returns the mass type of the parent (0 - monoisotopic, 1 - average mass)
`getMatchPeakAllowedError`(self)	Returns the number of top abundant peaks that are allowed not to match with a theoretical peak
`getMatchPeakCount`(self)	Returns the number of top abundant peaks to match with theoretical ones
`getMatchPeakTolerance`(self)	Returns the match peak tolerance
`getMaxAAPerModPerPeptide`(self)	Returns the maximum number of amino acids containing the same modification in a peptide
`getMaxInternalCleavageSites`(self)	Returns the maximum number of internal cleavage sites
`getMaxModsPerPeptide`(self)	Returns the maximum number of modifications that are allowed in a peptide
`getModifications`
`getNeutralLossesForIons`(self)	Returns whether neutral losses are considered for the a-, b- and y-ions
`getNormalizeXcorr`(self)	Returns whether normalized xcorr values are displayed
`getNucleotideReadingFrame`(self)	Returns the nucleotide reading frame
`getOutputLines`(self)	Returns the number of peptides to be displayed
`getPartialSequence`(self)	Returns the partial sequences (space delimited) that have to occur in the theoretical spectra
`getPeakMassTolerance`(self)	Returns the peak mass tolerance
`getPeptideMassUnit`(self)	Returns the peptide mass unit
`getPrecursorMassTolerance`(self)	Returns the precursor mass tolerance
`getPrintDuplicateReferences`(self)	Returns whether all proteins containing a found peptide should be displayed
`getProteinMassFilter`(self)	Returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)
`getRemovePrecursorNearPeaks`(self)	Returns whether peaks near (15 amu) the precursor peak are removed
`getResiduesInUpperCase`(self)	Returns whether residues are in upper case
`getSequenceHeaderFilter`(self)	Returns the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered
`getShowFragmentIons`(self)	Returns whether fragment ions shall be displayed
`handlePTMs`(self, modification_line, ...)
`setDatabase`(self, database)	Sets the used database
`setEnzyme`(self, enzyme_name)	Sets the enzyme used for cleavage (by means of the number from a list of enzymes)
`setIonCutoffPercentage`(self, ...)	Sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks
`setIonSeriesWeights`(self, ion_series_weights)	Sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
`setMassTypeFragment`(self, mass_type_fragment)	Sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)
`setMassTypeParent`(self, mass_type_parent)	Sets the mass type of the parent (0 - monoisotopic, 1 - average mass)
`setMatchPeakAllowedError`(self, ...)	Sets the number of top abundant peaks that are allowed not to match with a theoretical peak
`setMatchPeakCount`(self, match_peak_count)	Sets the number of top abundant peaks to with theoretical ones
`setMatchPeakTolerance`(self, match_peak_tolerance)	Sets the match peak tolerance
`setMaxAAPerModPerPeptide`(self, ...)	Sets the maximum number of amino acids containing the same modification in a peptide
`setMaxInternalCleavageSites`(self, ...)	Sets the maximum number of internal cleavage sites
`setMaxModsPerPeptide`(self, max_mods_per_peptide)	Sets the maximum number of modifications that are allowed in a peptide
`setNeutralLossesForIons`(self, ...)	Sets whether neutral losses are considered for the a-, b- and y-ions
`setNormalizeXcorr`(self, normalize_xcorr)	Sets whether normalized xcorr values are displayed
`setNucleotideReadingFrame`(self, ...)	Sets the nucleotide reading frame
`setOutputLines`(self, output_lines)	Sets the number of peptides to be displayed
`setPartialSequence`(self, partial_sequence)	Sets the partial sequences (space delimited) that have to occur in the theoretical spectra
`setPeakMassTolerance`(self, peak_mass_tolerance)	Sets the peak mass tolerance
`setPeptideMassUnit`(self, peptide_mass_unit)	Sets the peptide mass unit
`setPrecursorMassTolerance`(self, ...)	Sets the precursor mass tolerance
`setPrintDuplicateReferences`(self, ...)	Sets whether all proteins containing a found peptide should be displayed
`setProteinMassFilter`(self, protein_mass_filter)	Sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)
`setRemovePrecursorNearPeaks`(self, ...)	Sets whether peaks near (15 amu) the precursor peak are removed
`setResiduesInUpperCase`(self, ...)	Sets whether residues are in upper case
`setSequenceHeaderFilter`(self, ...)	Sets the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered
`setShowFragmentIons`(self, show_fragments)	Sets whether fragment ions shall be displayed
`store`(self, filename)	Stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution

addEnzymeInfo(self, enzyme_info: List[bytes]) → None: Adds an enzyme to the list and sets is as used

getDatabase(self) → Union[bytes, str, String]: Returns the used database

getEnzymeInfoAsString(self) → Union[bytes, str, String]: Returns the enzyme list as a string

getEnzymeName(self) → Union[bytes, str, String]: Returns the enzyme used for cleavage

getEnzymeNumber(self) → int: Returns the enzyme used for cleavage (by means of the number from a list of enzymes)

getIonCutoffPercentage(self) → float: Returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks

getIonSeriesWeights(self) → Union[bytes, str, String]: Returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

getMassTypeFragment(self) → bool: Returns the mass type of the fragments (0 - monoisotopic, 1 - average mass)

getMassTypeParent(self) → bool: Returns the mass type of the parent (0 - monoisotopic, 1 - average mass)

getMatchPeakAllowedError(self) → int: Returns the number of top abundant peaks that are allowed not to match with a theoretical peak

getMatchPeakCount(self) → int: Returns the number of top abundant peaks to match with theoretical ones

getMatchPeakTolerance(self) → float: Returns the match peak tolerance

getMaxAAPerModPerPeptide(self) → int: Returns the maximum number of amino acids containing the same modification in a peptide

getMaxInternalCleavageSites(self) → int: Returns the maximum number of internal cleavage sites

getMaxModsPerPeptide(self) → int: Returns the maximum number of modifications that are allowed in a peptide

getModifications()

getNeutralLossesForIons(self) → Union[bytes, str, String]: Returns whether neutral losses are considered for the a-, b- and y-ions

getNormalizeXcorr(self) → bool: Returns whether normalized xcorr values are displayed

getNucleotideReadingFrame(self) → int: Returns the nucleotide reading frame

getOutputLines(self) → int: Returns the number of peptides to be displayed

getPartialSequence(self) → Union[bytes, str, String]: Returns the partial sequences (space delimited) that have to occur in the theoretical spectra

getPeakMassTolerance(self) → float: Returns the peak mass tolerance

getPeptideMassUnit(self) → int: Returns the peptide mass unit

getPrecursorMassTolerance(self) → float: Returns the precursor mass tolerance

getPrintDuplicateReferences(self) → bool: Returns whether all proteins containing a found peptide should be displayed

getProteinMassFilter(self) → Union[bytes, str, String]: Returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)

getRemovePrecursorNearPeaks(self) → bool: Returns whether peaks near (15 amu) the precursor peak are removed

getResiduesInUpperCase(self) → bool: Returns whether residues are in upper case

getSequenceHeaderFilter(self) → Union[bytes, str, String]: Returns the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered

getShowFragmentIons(self) → bool: Returns whether fragment ions shall be displayed

handlePTMs(self, modification_line: Union[bytes, str, String], modifications_filename: Union[bytes, str, String], monoisotopic: bool) → None

setDatabase(self, database: Union[bytes, str, String]) → None: Sets the used database

setEnzyme(self, enzyme_name: Union[bytes, str, String]) → int: Sets the enzyme used for cleavage (by means of the number from a list of enzymes)

setIonCutoffPercentage(self, ion_cutoff_percentage: float) → None: Sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks

setIonSeriesWeights(self, ion_series_weights: Union[bytes, str, String]) → None: Sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

setMassTypeFragment(self, mass_type_fragment: bool) → None: Sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)

setMassTypeParent(self, mass_type_parent: bool) → None: Sets the mass type of the parent (0 - monoisotopic, 1 - average mass)

setMatchPeakAllowedError(self, match_peak_allowed_error: int) → None: Sets the number of top abundant peaks that are allowed not to match with a theoretical peak

setMatchPeakCount(self, match_peak_count: int) → None: Sets the number of top abundant peaks to with theoretical ones

setMatchPeakTolerance(self, match_peak_tolerance: float) → None: Sets the match peak tolerance

setMaxAAPerModPerPeptide(self, max_aa_per_mod_per_peptide: int) → None: Sets the maximum number of amino acids containing the same modification in a peptide

setMaxInternalCleavageSites(self, max_internal_cleavage_sites: int) → None: Sets the maximum number of internal cleavage sites

setMaxModsPerPeptide(self, max_mods_per_peptide: int) → None: Sets the maximum number of modifications that are allowed in a peptide

setNeutralLossesForIons(self, neutral_losses_for_ions: Union[bytes, str, String]) → None: Sets whether neutral losses are considered for the a-, b- and y-ions

setNormalizeXcorr(self, normalize_xcorr: bool) → None: Sets whether normalized xcorr values are displayed

setNucleotideReadingFrame(self, nucleotide_reading_frame: int) → None: Sets the nucleotide reading frame

setOutputLines(self, output_lines: int) → None: Sets the number of peptides to be displayed

setPartialSequence(self, partial_sequence: Union[bytes, str, String]) → None: Sets the partial sequences (space delimited) that have to occur in the theoretical spectra

setPeakMassTolerance(self, peak_mass_tolerance: float) → None: Sets the peak mass tolerance

setPeptideMassUnit(self, peptide_mass_unit: int) → None: Sets the peptide mass unit

setPrecursorMassTolerance(self, precursor_mass_tolerance: float) → None: Sets the precursor mass tolerance

setPrintDuplicateReferences(self, print_duplicate_references: bool) → None: Sets whether all proteins containing a found peptide should be displayed

setProteinMassFilter(self, protein_mass_filter: Union[bytes, str, String]) → None: Sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)

setRemovePrecursorNearPeaks(self, remove_precursor_near_peaks: bool) → None: Sets whether peaks near (15 amu) the precursor peak are removed

setResiduesInUpperCase(self, residues_in_upper_case: bool) → None: Sets whether residues are in upper case

setSequenceHeaderFilter(self, sequence_header_filter: Union[bytes, str, String]) → None: Sets the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered

setShowFragmentIons(self, show_fragments: bool) → None: Sets whether fragment ions shall be displayed

store(self, filename: Union[bytes, str, String]) → None

Stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution

Parameters: filename – the name of the file in which the infile is stored into