ProtonDistributionModel

class pyopenms.ProtonDistributionModel

Bases: object

Cython implementation of _ProtonDistributionModel

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

A proton distribution model to calculate the proton distribution over charged peptides

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__()

Overload:

__init__(self) → None

A proton distribution model to calculate the proton distribution over charged peptides

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

Overload:

__init__(self, in_0: ProtonDistributionModel) → None

Methods

__init__	Overload:
getChargeStateIntensities(self, peptide, ...)	Calculates the charge state intensities of different charge states of the same ion
getDefaults(self)	Returns the default parameters
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getProtonDistribution(self, bb_charges, ...)	Calculates a proton distribution of the given charged peptide
getSubsections(self)
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters
setPeptideProtonDistribution(self, ...)

FragmentationType

alias of __FragmentationType

getChargeStateIntensities(self, peptide: AASequence, n_term_ion: AASequence, c_term_ion: AASequence, charge: int, n_term_type: int, n_term_intensities: List[float], c_term_intensities: List[float], type_: int) → None

Calculates the charge state intensities of different charge states of the same ion

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(self) → Param

Returns the default parameters

getName(self) → bytes | str | String

Returns the name

getParameters(self) → Param

Returns the parameters

getProtonDistribution(self, bb_charges: List[float], sc_charges: List[float], peptide: AASequence, charge: int, res_type: int) → None

Calculates a proton distribution of the given charged peptide

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

• peptide – The peptide as AASequence object

• charge – The charge

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

getSubsections(self) → List[bytes]

setName(self, in_0: bytes | str | String) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters

setPeptideProtonDistribution(self, bb_charge: List[float], sc_charge: List[float]) → None