ProtonDistributionModel

class pyopenms.ProtonDistributionModel

Bases: object

Cython implementation of _ProtonDistributionModel

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ProtonDistributionModel.html

– Inherits from [‘DefaultParamHandler’]

The model uses proton affinity values of backbone nitrogens and sidechains to calculate the proton distribution of charged peptide among these sites. The possible sites are the peptide bonds between the amino acids, the side chains and the C-terminus and N-terminus. The calculation is done calculating a Boltzmann distribution of the sites —– Details and the proton affinities can be found in Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004 —– A proton distribution can be calculated using the getProtonDistribution method. The backbone probabilities are reported in the first parameter (index 0 for the N-terminus, index 1 for the first peptide bond…), the site chain probabilities are reported in the second parameter (index 0, for the first amino acid…). The peptide and the number of protons as well as type of peptide (can be Reside::YIon for peptides and y-ions and any other ion type) —– Charge state intensities of differently charged equal (e.g. y7+ and y7++) ions can be calculated using the getChargeStateIntensities function

__init__()

• Cython signature: void ProtonDistributionModel()

The model uses proton affinity values of backbone nitrogens and sidechains to calculate the proton distribution of charged peptide among these sites. The possible sites are the peptide bonds between the amino acids, the side chains and the C-terminus and N-terminus. The calculation is done calculating a Boltzmann distribution of the sites —– Details and the proton affinities can be found in Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004 —– A proton distribution can be calculated using the getProtonDistribution method. The backbone probabilities are reported in the first parameter (index 0 for the N-terminus, index 1 for the first peptide bond…), the site chain probabilities are reported in the second parameter (index 0, for the first amino acid…). The peptide and the number of protons as well as type of peptide (can be Reside::YIon for peptides and y-ions and any other ion type) —– Charge state intensities of differently charged equal (e.g. y7+ and y7++) ions can be calculated using the getChargeStateIntensities function

• Cython signature: void ProtonDistributionModel(ProtonDistributionModel &)

Methods

__init__	Cython signature: void ProtonDistributionModel()
getChargeStateIntensities	Cython signature: void getChargeStateIntensities(AASequence & peptide, AASequence & n_term_ion, AASequence & c_term_ion, int charge, ResidueType n_term_type, libcpp_vector[double] & n_term_intensities, libcpp_vector[double] & c_term_intensities, FragmentationType type_)
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getProtonDistribution	Cython signature: void getProtonDistribution(libcpp_vector[double] & bb_charges, libcpp_vector[double] & sc_charges, AASequence & peptide, int charge, ResidueType res_type)
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters
setPeptideProtonDistribution	Cython signature: void setPeptideProtonDistribution(libcpp_vector[double] & bb_charge, libcpp_vector[double] & sc_charge)

FragmentationType

alias of pyopenms.pyopenms_6.__FragmentationType

getChargeStateIntensities()

Cython signature: void getChargeStateIntensities(AASequence & peptide, AASequence & n_term_ion, AASequence & c_term_ion, int charge, ResidueType n_term_type, libcpp_vector[double] & n_term_intensities, libcpp_vector[double] & c_term_intensities, FragmentationType type_)

Parameters

• peptide – The peptide

• n_term_ion – The prefix ion sequence

• c_term_ion – The suffix ion sequence

• charge – The charge

• n_term_type – The ion type of the N-terminal ion; valid values are Residue::AIon, Residue::BIon

• n_term_intensities – The probability of seeing a charged prefix ions (first index corresponds to ion of charge 1)

• c_term_intensities – The probability of seeing a charged suffix ions (first index corresponds to ion of charge 2)

• type – The type of fragmentation (charge-directed, charge-remote of side chain)

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getProtonDistribution()

Cython signature: void getProtonDistribution(libcpp_vector[double] & bb_charges, libcpp_vector[double] & sc_charges, AASequence & peptide, int charge, ResidueType res_type)

Parameters

• bb_charges – The calculated probabilities of the backbone sites (including N-terminus and C-terminus)

• sc_charges – The calculated probabilities of the side chain sites

:param peptide The peptide :param charge The charge :param res_type: The type of the ion given in peptide. Peptides are handled as y-ions, i.e. Residue::YIon

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

setPeptideProtonDistribution()

Cython signature: void setPeptideProtonDistribution(libcpp_vector[double] & bb_charge, libcpp_vector[double] & sc_charge)