IMSIsotopeDistribution

class pyopenms.IMSIsotopeDistribution

Bases: object

Cython implementation of _IMSIsotopeDistribution

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS::ims::IMSIsotopeDistribution_1_1IMSIsotopeDistribution.html

Represents a distribution of isotopes of chemical elements as a list of peaks each as a pair of mass and abundance. ‘IsotopeDistribution’ unlike ‘IsotopeSpecies’ has one abundance per a nominal mass. Here is an example in the format (mass; abundance %) for molecule H2O (values are taken randomly): —– - IsotopeDistribution

(18.00221; 99.03 %) (19.00334; 0.8 %) (20.00476; 0.17 %)

  • IsotopeSpecies

    (18.00197; 98.012 %) (18.00989; 1.018 %) (19.00312; 0.683 %) (19.00531; 0.117 %) (20.00413; 0.134 %) (20.00831; 0.036 %)

To the sake of faster computations distribution is restricted to the first K elements, where K can be set by adjusting size ‘SIZE’ of distribution. @note For the elements most abundant in living beings (CHNOPS) this restriction is negligible, since abundances decrease dramatically in isotopes order and are usually of no interest starting from +10 isotope. —– ‘IsotopeDistribution’ implements folding with other distribution using an algorithm described in details in paper: Boecker et al. “Decomposing metabolic isotope patterns” WABI 2006. doi: 10.1007/11851561_2 —– Folding with itself is done using Russian Multiplication Scheme

__init__()

  • Cython signature: void IMSIsotopeDistribution()

  • Cython signature: void IMSIsotopeDistribution(IMSIsotopeDistribution &)

  • Cython signature: void IMSIsotopeDistribution(unsigned int nominalMass)

  • Cython signature: void IMSIsotopeDistribution(double mass)

  • Cython signature: void IMSIsotopeDistribution(libcpp_vector[IMSIsotopeDistribution_Peak] & peaks, unsigned int nominalMass)

Methods

__init__

  • Cython signature: void IMSIsotopeDistribution()

empty

Cython signature: bool empty() Returns true if the distribution has no peaks, false - otherwise

getAbundance

Cython signature: double getAbundance(int i)

getAbundances

Cython signature: libcpp_vector[double] getAbundances() Gets an abundance of isotope 'i'

getAverageMass

Cython signature: double getAverageMass()

getMass

Cython signature: double getMass(int i)

getMasses

Cython signature: libcpp_vector[double] getMasses() Gets a mass of isotope 'i'

getNominalMass

Cython signature: unsigned int getNominalMass()

normalize

Cython signature: void normalize() Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error.

setNominalMass

Cython signature: void setNominalMass(unsigned int nominalMass)

size

Cython signature: int size()

Attributes

ABUNDANCES_SUM_ERROR

SIZE

ABUNDANCES_SUM_ERROR
SIZE
empty()

Cython signature: bool empty() Returns true if the distribution has no peaks, false - otherwise

getAbundance()

Cython signature: double getAbundance(int i)

getAbundances()

Cython signature: libcpp_vector[double] getAbundances() Gets an abundance of isotope ‘i’

getAverageMass()

Cython signature: double getAverageMass()

getMass()

Cython signature: double getMass(int i)

getMasses()

Cython signature: libcpp_vector[double] getMasses() Gets a mass of isotope ‘i’

getNominalMass()

Cython signature: unsigned int getNominalMass()

normalize()

Cython signature: void normalize() Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error

setNominalMass()

Cython signature: void setNominalMass(unsigned int nominalMass)

size()

Cython signature: int size()