IsotopeDistribution

class pyopenms.IsotopeDistribution

Bases: object

Cython implementation of _IsotopeDistribution

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1IsotopeDistribution.html

A container that holds an isotope distribution. It consists of mass values and their correspondent probabilities (stored in the intensity slot) —– Isotope distributions can be calculated using either the CoarseIsotopePatternGenerator for quantized atomic masses which group isotopes with the same atomic number. Alternatively, the FineIsotopePatternGenerator can be used that calculates hyperfine isotopic distributions

This class only describes the container that holds the isotopic distribution, calculations are done using classes derived from IsotopePatternGenerator

__init__()

• Cython signature: void IsotopeDistribution()

• Cython signature: void IsotopeDistribution(IsotopeDistribution &)

Methods

__init__	Cython signature: void IsotopeDistribution()
averageMass	Cython signature: double averageMass() Compute average mass of isotope distribution (weighted average of all isotopes)
clear	Cython signature: void clear() Clears the distribution and resets max isotope to 0
getContainer	Cython signature: libcpp_vector[Peak1D] & getContainer() Returns the container which holds the distribution
getMax	Cython signature: size_t getMax() Returns the maximal weight isotope which is stored in the distribution
getMin	Cython signature: size_t getMin() Returns the minimal weight isotope which is stored in the distribution
getMostAbundant	Cython signature: Peak1D getMostAbundant() Returns the most abundant isotope which is stored in the distribution
insert	Cython signature: void insert(double mass, float intensity)
merge	Cython signature: void merge(double, double) Merges distributions of arbitrary data points with constant defined resolution
renormalize	Cython signature: void renormalize() Renormalizes the sum of the probabilities of the isotopes to 1
resize	Cython signature: void resize(unsigned int size) Resizes distribution container
set	Cython signature: void set(libcpp_vector[Peak1D] & distribution) Overwrites the container which holds the distribution using 'distribution'
size	Cython signature: size_t size() Returns the size of the distribution which is the number of isotopes in the distribution
sortByIntensity	Cython signature: void sortByIntensity() Sort isotope distribution by intensity
sortByMass	Cython signature: void sortByMass() Sort isotope distribution by mass
trimIntensities	Cython signature: void trimIntensities(double cutoff) Remove intensities below the cutoff
trimLeft	Cython signature: void trimLeft(double cutoff) Trims the left side of the isotope distribution to isotopes with a significant contribution
trimRight	Cython signature: void trimRight(double cutoff) Trims the right side of the isotope distribution to isotopes with a significant contribution

Sorted

alias of pyopenms.pyopenms_8.__Sorted

averageMass()

Cython signature: double averageMass() Compute average mass of isotope distribution (weighted average of all isotopes)

clear()

Cython signature: void clear() Clears the distribution and resets max isotope to 0

getContainer()

Cython signature: libcpp_vector[Peak1D] & getContainer() Returns the container which holds the distribution

getMax()

Cython signature: size_t getMax() Returns the maximal weight isotope which is stored in the distribution

getMin()

Cython signature: size_t getMin() Returns the minimal weight isotope which is stored in the distribution

getMostAbundant()

Cython signature: Peak1D getMostAbundant() Returns the most abundant isotope which is stored in the distribution

insert()

Cython signature: void insert(double mass, float intensity)

merge()

Cython signature: void merge(double, double) Merges distributions of arbitrary data points with constant defined resolution

renormalize()

Cython signature: void renormalize() Renormalizes the sum of the probabilities of the isotopes to 1

resize()

Cython signature: void resize(unsigned int size) Resizes distribution container

set()

Cython signature: void set(libcpp_vector[Peak1D] & distribution) Overwrites the container which holds the distribution using ‘distribution’

size()

Cython signature: size_t size() Returns the size of the distribution which is the number of isotopes in the distribution

sortByIntensity()

Cython signature: void sortByIntensity() Sort isotope distribution by intensity

sortByMass()

Cython signature: void sortByMass() Sort isotope distribution by mass

trimIntensities()

Cython signature: void trimIntensities(double cutoff) Remove intensities below the cutoff

trimLeft()

Cython signature: void trimLeft(double cutoff) Trims the left side of the isotope distribution to isotopes with a significant contribution

trimRight()

Cython signature: void trimRight(double cutoff) Trims the right side of the isotope distribution to isotopes with a significant contribution