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
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
Returns the maximum number of internal cleavage sites
getMaxModsPerPeptide
(self)Returns the maximum number of modifications that are allowed in a peptide
getNeutralLossesForIons
(self)Returns whether neutral losses are considered for the a-, b- and y-ions
getNormalizeXcorr
(self)Returns whether normalized xcorr values are displayed
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
Returns the precursor mass tolerance
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)
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
- 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) 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) 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) 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) 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) 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: bytes | str | String, modifications_filename: bytes | str | String, monoisotopic: bool) None #
- setEnzyme(self, enzyme_name: 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: 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: 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: 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: 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: 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