SequestInfile#
- class pyopenms.SequestInfile#
Bases:
objectCython implementation of _SequestInfile
Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SequestInfile.html
- __init__()#
Cython signature: void SequestInfile() Sequest input file adapter
Cython signature: void SequestInfile(SequestInfile &)
Methods
Cython signature: void SequestInfile()
Cython signature: void addEnzymeInfo(libcpp_vector[String] & enzyme_info) Adds an enzyme to the list and sets is as used
Cython signature: String getDatabase() Returns the used database
Cython signature: String getEnzymeInfoAsString() Returns the enzyme list as a string
Cython signature: String getEnzymeName() Returns the enzyme used for cleavage
Cython signature: size_t getEnzymeNumber() Returns the enzyme used for cleavage (by means of the number from a list of enzymes)
Cython signature: float getIonCutoffPercentage() Returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks
Cython signature: String getIonSeriesWeights() Returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
Cython signature: bool getMassTypeFragment() Returns the mass type of the fragments (0 - monoisotopic, 1 - average mass)
Cython signature: bool getMassTypeParent() Returns the mass type of the parent (0 - monoisotopic, 1 - average mass)
Cython signature: size_t getMatchPeakAllowedError() Returns the number of top abundant peaks that are allowed not to match with a theoretical peak
Cython signature: size_t getMatchPeakCount() Returns the number of top abundant peaks to match with theoretical ones
Cython signature: float getMatchPeakTolerance() Returns the match peak tolerance
Cython signature: size_t getMaxAAPerModPerPeptide() Returns the maximum number of amino acids containing the same modification in a peptide
Cython signature: size_t getMaxInternalCleavageSites() Returns the maximum number of internal cleavage sites
Cython signature: size_t getMaxModsPerPeptide() Returns the maximum number of modifications that are allowed in a peptide
Cython signature: String getNeutralLossesForIons() Returns whether neutral losses are considered for the a-, b- and y-ions
Cython signature: bool getNormalizeXcorr() Returns whether normalized xcorr values are displayed
Cython signature: size_t getNucleotideReadingFrame() Returns the nucleotide reading frame
Cython signature: size_t getOutputLines() Returns the number of peptides to be displayed
Cython signature: String getPartialSequence() Returns the partial sequences (space delimited) that have to occur in the theoretical spectra
Cython signature: float getPeakMassTolerance() Returns the peak mass tolerance
Cython signature: size_t getPeptideMassUnit() Returns the peptide mass unit
Cython signature: float getPrecursorMassTolerance() Returns the precursor mass tolerance
Cython signature: bool getPrintDuplicateReferences() Returns whether all proteins containing a found peptide should be displayed
Cython signature: String getProteinMassFilter() Returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)
Cython signature: bool getRemovePrecursorNearPeaks() Returns whether peaks near (15 amu) the precursor peak are removed
Cython signature: bool getResiduesInUpperCase() Returns whether residues are in upper case
Cython signature: String getSequenceHeaderFilter() 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
Cython signature: bool getShowFragmentIons() Returns whether fragment ions shall be displayed
Cython signature: void handlePTMs(const String & modification_line, const String & modifications_filename, bool monoisotopic)
Cython signature: void setDatabase(const String & database) Sets the used database
Cython signature: size_t setEnzyme(String enzyme_name) Sets the enzyme used for cleavage (by means of the number from a list of enzymes)
Cython signature: void setIonCutoffPercentage(float ion_cutoff_percentage) Sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks
Cython signature: void setIonSeriesWeights(const String & ion_series_weights) Sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
Cython signature: void setMassTypeFragment(bool mass_type_fragment) Sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)
Cython signature: void setMassTypeParent(bool mass_type_parent) Sets the mass type of the parent (0 - monoisotopic, 1 - average mass)
Cython signature: void setMatchPeakAllowedError(size_t match_peak_allowed_error) Sets the number of top abundant peaks that are allowed not to match with a theoretical peak
Cython signature: void setMatchPeakCount(size_t match_peak_count) Sets the number of top abundant peaks to with theoretical ones
Cython signature: void setMatchPeakTolerance(float match_peak_tolerance) Sets the match peak tolerance
Cython signature: void setMaxAAPerModPerPeptide(size_t max_aa_per_mod_per_peptide) Sets the maximum number of amino acids containing the same modification in a peptide
Cython signature: void setMaxInternalCleavageSites(size_t max_internal_cleavage_sites) Sets the maximum number of internal cleavage sites
Cython signature: void setMaxModsPerPeptide(size_t max_mods_per_peptide) Sets the maximum number of modifications that are allowed in a peptide
Cython signature: void setNeutralLossesForIons(const String & neutral_losses_for_ions) Sets whether neutral losses are considered for the a-, b- and y-ions
Cython signature: void setNormalizeXcorr(bool normalize_xcorr) Sets whether normalized xcorr values are displayed
Cython signature: void setNucleotideReadingFrame(size_t nucleotide_reading_frame) Sets the nucleotide reading frame
Cython signature: void setOutputLines(size_t output_lines) Sets the number of peptides to be displayed
Cython signature: void setPartialSequence(const String & partial_sequence) Sets the partial sequences (space delimited) that have to occur in the theoretical spectra
Cython signature: void setPeakMassTolerance(float peak_mass_tolerance) Sets the peak mass tolerance
Cython signature: void setPeptideMassUnit(size_t peptide_mass_unit) Sets the peptide mass unit
Cython signature: void setPrecursorMassTolerance(float precursor_mass_tolerance) Sets the precursor mass tolerance
Cython signature: void setPrintDuplicateReferences(bool print_duplicate_references) Sets whether all proteins containing a found peptide should be displayed
Cython signature: void setProteinMassFilter(const String & protein_mass_filter) Sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)
Cython signature: void setRemovePrecursorNearPeaks(bool remove_precursor_near_peaks) Sets whether peaks near (15 amu) the precursor peak are removed
Cython signature: void setResiduesInUpperCase(bool residues_in_upper_case) Sets whether residues are in upper case
Cython signature: void setSequenceHeaderFilter(const String & sequence_header_filter) 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
Cython signature: void setShowFragmentIons(bool show_fragments) Sets whether fragment ions shall be displayed
Cython signature: void store(const String & filename)
- addEnzymeInfo()#
Cython signature: void addEnzymeInfo(libcpp_vector[String] & enzyme_info) Adds an enzyme to the list and sets is as used
- getDatabase()#
Cython signature: String getDatabase() Returns the used database
- getEnzymeInfoAsString()#
Cython signature: String getEnzymeInfoAsString() Returns the enzyme list as a string
- getEnzymeName()#
Cython signature: String getEnzymeName() Returns the enzyme used for cleavage
- getEnzymeNumber()#
Cython signature: size_t getEnzymeNumber() Returns the enzyme used for cleavage (by means of the number from a list of enzymes)
- getIonCutoffPercentage()#
Cython signature: float getIonCutoffPercentage() Returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks
- getIonSeriesWeights()#
Cython signature: String getIonSeriesWeights() Returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
- getMassTypeFragment()#
Cython signature: bool getMassTypeFragment() Returns the mass type of the fragments (0 - monoisotopic, 1 - average mass)
- getMassTypeParent()#
Cython signature: bool getMassTypeParent() Returns the mass type of the parent (0 - monoisotopic, 1 - average mass)
- getMatchPeakAllowedError()#
Cython signature: size_t getMatchPeakAllowedError() Returns the number of top abundant peaks that are allowed not to match with a theoretical peak
- getMatchPeakCount()#
Cython signature: size_t getMatchPeakCount() Returns the number of top abundant peaks to match with theoretical ones
- getMatchPeakTolerance()#
Cython signature: float getMatchPeakTolerance() Returns the match peak tolerance
- getMaxAAPerModPerPeptide()#
Cython signature: size_t getMaxAAPerModPerPeptide() Returns the maximum number of amino acids containing the same modification in a peptide
- getMaxInternalCleavageSites()#
Cython signature: size_t getMaxInternalCleavageSites() Returns the maximum number of internal cleavage sites
- getMaxModsPerPeptide()#
Cython signature: size_t getMaxModsPerPeptide() Returns the maximum number of modifications that are allowed in a peptide
- getModifications()#
- getNeutralLossesForIons()#
Cython signature: String getNeutralLossesForIons() Returns whether neutral losses are considered for the a-, b- and y-ions
- getNormalizeXcorr()#
Cython signature: bool getNormalizeXcorr() Returns whether normalized xcorr values are displayed
- getNucleotideReadingFrame()#
Cython signature: size_t getNucleotideReadingFrame() Returns the nucleotide reading frame
- getOutputLines()#
Cython signature: size_t getOutputLines() Returns the number of peptides to be displayed
- getPartialSequence()#
Cython signature: String getPartialSequence() Returns the partial sequences (space delimited) that have to occur in the theoretical spectra
- getPeakMassTolerance()#
Cython signature: float getPeakMassTolerance() Returns the peak mass tolerance
- getPeptideMassUnit()#
Cython signature: size_t getPeptideMassUnit() Returns the peptide mass unit
- getPrecursorMassTolerance()#
Cython signature: float getPrecursorMassTolerance() Returns the precursor mass tolerance
- getPrintDuplicateReferences()#
Cython signature: bool getPrintDuplicateReferences() Returns whether all proteins containing a found peptide should be displayed
- getProteinMassFilter()#
Cython signature: String getProteinMassFilter() Returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)
- getRemovePrecursorNearPeaks()#
Cython signature: bool getRemovePrecursorNearPeaks() Returns whether peaks near (15 amu) the precursor peak are removed
- getResiduesInUpperCase()#
Cython signature: bool getResiduesInUpperCase() Returns whether residues are in upper case
- getSequenceHeaderFilter()#
Cython signature: String getSequenceHeaderFilter() 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()#
Cython signature: bool getShowFragmentIons() Returns whether fragment ions shall be displayed
- handlePTMs()#
Cython signature: void handlePTMs(const String & modification_line, const String & modifications_filename, bool monoisotopic)
- setDatabase()#
Cython signature: void setDatabase(const String & database) Sets the used database
- setEnzyme()#
Cython signature: size_t setEnzyme(String enzyme_name) Sets the enzyme used for cleavage (by means of the number from a list of enzymes)
- setIonCutoffPercentage()#
Cython signature: void setIonCutoffPercentage(float ion_cutoff_percentage) Sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks
- setIonSeriesWeights()#
Cython signature: void setIonSeriesWeights(const String & ion_series_weights) Sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
- setMassTypeFragment()#
Cython signature: void setMassTypeFragment(bool mass_type_fragment) Sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)
- setMassTypeParent()#
Cython signature: void setMassTypeParent(bool mass_type_parent) Sets the mass type of the parent (0 - monoisotopic, 1 - average mass)
- setMatchPeakAllowedError()#
Cython signature: void setMatchPeakAllowedError(size_t match_peak_allowed_error) Sets the number of top abundant peaks that are allowed not to match with a theoretical peak
- setMatchPeakCount()#
Cython signature: void setMatchPeakCount(size_t match_peak_count) Sets the number of top abundant peaks to with theoretical ones
- setMatchPeakTolerance()#
Cython signature: void setMatchPeakTolerance(float match_peak_tolerance) Sets the match peak tolerance
- setMaxAAPerModPerPeptide()#
Cython signature: void setMaxAAPerModPerPeptide(size_t max_aa_per_mod_per_peptide) Sets the maximum number of amino acids containing the same modification in a peptide
- setMaxInternalCleavageSites()#
Cython signature: void setMaxInternalCleavageSites(size_t max_internal_cleavage_sites) Sets the maximum number of internal cleavage sites
- setMaxModsPerPeptide()#
Cython signature: void setMaxModsPerPeptide(size_t max_mods_per_peptide) Sets the maximum number of modifications that are allowed in a peptide
- setNeutralLossesForIons()#
Cython signature: void setNeutralLossesForIons(const String & neutral_losses_for_ions) Sets whether neutral losses are considered for the a-, b- and y-ions
- setNormalizeXcorr()#
Cython signature: void setNormalizeXcorr(bool normalize_xcorr) Sets whether normalized xcorr values are displayed
- setNucleotideReadingFrame()#
Cython signature: void setNucleotideReadingFrame(size_t nucleotide_reading_frame) Sets the nucleotide reading frame
- setOutputLines()#
Cython signature: void setOutputLines(size_t output_lines) Sets the number of peptides to be displayed
- setPartialSequence()#
Cython signature: void setPartialSequence(const String & partial_sequence) Sets the partial sequences (space delimited) that have to occur in the theoretical spectra
- setPeakMassTolerance()#
Cython signature: void setPeakMassTolerance(float peak_mass_tolerance) Sets the peak mass tolerance
- setPeptideMassUnit()#
Cython signature: void setPeptideMassUnit(size_t peptide_mass_unit) Sets the peptide mass unit
- setPrecursorMassTolerance()#
Cython signature: void setPrecursorMassTolerance(float precursor_mass_tolerance) Sets the precursor mass tolerance
- setPrintDuplicateReferences()#
Cython signature: void setPrintDuplicateReferences(bool print_duplicate_references) Sets whether all proteins containing a found peptide should be displayed
- setProteinMassFilter()#
Cython signature: void setProteinMassFilter(const String & protein_mass_filter) Sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)
- setRemovePrecursorNearPeaks()#
Cython signature: void setRemovePrecursorNearPeaks(bool remove_precursor_near_peaks) Sets whether peaks near (15 amu) the precursor peak are removed
- setResiduesInUpperCase()#
Cython signature: void setResiduesInUpperCase(bool residues_in_upper_case) Sets whether residues are in upper case
- setSequenceHeaderFilter()#
Cython signature: void setSequenceHeaderFilter(const String & sequence_header_filter) 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()#
Cython signature: void setShowFragmentIons(bool show_fragments) Sets whether fragment ions shall be displayed
- store()#
Cython signature: void store(const String & filename)
- Parameters
filename – the name of the file in which the infile is stored into