Tagger

class pyopenms.Tagger

Bases: object

Cython implementation of _Tagger

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1Tagger.html

The parameter max_charge_ should be >= min_charge_ Also max_tag_length should be >= min_tag_length —– :param min_tag_length: The minimal sequence tag length :param ppm: The tolerance for matching residue masses to peak delta masses :param max_tag_length: The maximal sequence tag length :param min_charge: Minimal fragment charge considered for each sequence tag :param max_charge: Maximal fragment charge considered for each sequence tag :param fixed_mods: A list of modification names. The modified residues replace the unmodified versions :param var_mods: A list of modification names. The modified residues are added as additional entries to the list of residues

__init__()

  • Cython signature: void Tagger(Tagger &)

  • Cython signature: void Tagger(size_t min_tag_length, double ppm, size_t max_tag_length, size_t min_charge, size_t max_charge, const StringList & fixed_mods, const StringList & var_mods)

Methods

__init__

  • Cython signature: void Tagger(Tagger &)

getTag

  • Cython signature: void getTag(const libcpp_vector[double] & mzs, libcpp_vector[libcpp_utf8_string] & tags)

setMaxCharge

Cython signature: void setMaxCharge(size_t max_charge)
getTag()

  • Cython signature: void getTag(const libcpp_vector[double] & mzs, libcpp_vector[libcpp_utf8_string] & tags)

The parameter tags is filled with one string per sequence tag It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor —– :param mzs: A vector of mz values, containing the mz values from a centroided fragment spectrum :param tags: The vector of tags, that is filled with this function

  • Cython signature: void getTag(const MSSpectrum & spec, libcpp_vector[libcpp_utf8_string] & tags)

The parameter tags is filled with one string per sequence tag It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor —– :param spec: A centroided fragment spectrum :param tags: The vector of tags, that is filled with this function

setMaxCharge()

Cython signature: void setMaxCharge(size_t max_charge)

Allows to change the maximal considered charge e.g. based on a spectra precursor charge without calling the constructor multiple times —– :param max_charge: The new maximal charge