IsotopeModel

class pyopenms.IsotopeModel

Bases: object

Cython implementation of _IsotopeModel

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1IsotopeModel.html

This models a smoothed (widened) distribution, i.e. can be used to sample actual raw peaks (depending on the points you query) If you only want the distribution (no widening), use either EmpiricalFormula::getIsotopeDistribution() // for a certain sum formula or IsotopeDistribution::estimateFromPeptideWeight (double average_weight) // for averagine —– Peak widening is achieved by either a Gaussian or Lorentzian shape

__init__()

  • Cython signature: void IsotopeModel()

  • Cython signature: void IsotopeModel(IsotopeModel &)

Methods

__init__

  • Cython signature: void IsotopeModel()

getCenter

Cython signature: double getCenter()

getCharge

Cython signature: unsigned int getCharge()

getFormula

Cython signature: EmpiricalFormula getFormula() Return the Averagine peptide formula (mass calculated from mean mass and charge -- use .setParameters() to set them)

getIsotopeDistribution

Cython signature: IsotopeDistribution getIsotopeDistribution()

getOffset

Cython signature: double getOffset() Get the offset of the model

getProductName

Cython signature: String getProductName() Name of the model (needed by Factory)

setOffset

Cython signature: void setOffset(double offset)

setSamples

Cython signature: void setSamples(EmpiricalFormula & formula) Set sample/supporting points of interpolation
Averagines

alias of pyopenms.pyopenms_3.__Averagines

getCenter()

Cython signature: double getCenter()

This is a m/z-value not necessarily the monoisotopic mass

getCharge()

Cython signature: unsigned int getCharge()

getFormula()

Cython signature: EmpiricalFormula getFormula() Return the Averagine peptide formula (mass calculated from mean mass and charge – use .setParameters() to set them)

getIsotopeDistribution()

Cython signature: IsotopeDistribution getIsotopeDistribution()

Useful to determine the number of isotopes that the model contains and their position

getOffset()

Cython signature: double getOffset() Get the offset of the model

getProductName()

Cython signature: String getProductName() Name of the model (needed by Factory)

setOffset()

Cython signature: void setOffset(double offset)

The whole model will be shifted to the new offset without being computing all over This leaves a discrepancy which is minor in small shifts (i.e. shifting by one or two standard deviations) but can get significant otherwise. In that case use setParameters() which enforces a recomputation of the model

setSamples()

Cython signature: void setSamples(EmpiricalFormula & formula) Set sample/supporting points of interpolation