IMSIsotopeDistribution#
- class pyopenms.IMSIsotopeDistribution#
Bases:
object
Cython implementation of _IMSIsotopeDistribution
Original C++ documentation is available here
Represents a distribution of isotopes restricted to the first K elements
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__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: IMSIsotopeDistribution) None
Overload:
- __init__(self, nominalMass: int) None
Overload:
- __init__(self, mass: float) None
Overload:
- __init__(self, peaks: List[IMSIsotopeDistribution_Peak], nominalMass: int) None
Methods
Overload:
empty
(self)Returns true if the distribution has no peaks, false - otherwise
getAbundance
(self, i)getAbundances
(self)Gets an abundance of isotope 'i'
getAverageMass
(self)getMass
(self, i)getMasses
(self)Gets a mass of isotope 'i'
getNominalMass
(self)normalize
(self)Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error.
setNominalMass
(self, nominalMass)size
(self)Attributes
- ABUNDANCES_SUM_ERROR#
- SIZE#
- empty(self) bool #
Returns true if the distribution has no peaks, false - otherwise
- getAbundance(self, i: int) float #
- getAbundances(self) List[float] #
Gets an abundance of isotope ‘i’
- getAverageMass(self) float #
- getMass(self, i: int) float #
- getMasses(self) List[float] #
Gets a mass of isotope ‘i’
- getNominalMass(self) int #
- normalize(self) None #
Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error
- setNominalMass(self, nominalMass: int) None #
- size(self) int #