EmpiricalFormula

class pyopenms.EmpiricalFormula

Bases: object

Cython implementation of _EmpiricalFormula

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Representation of an empirical formula

Overload:

__init__(self, in_0: EmpiricalFormula) → None

Overload:

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

EmpiricalFormula Constructor from string

Overload:

__init__(self, number: int, element: Element, charge: int) → None

EmpiricalFormula Constructor with element pointer and number

Methods

__init__	Overload:
calculateTheoreticalIsotopesNumber(self)
contains(self, ef)	Returns true if all elements from ef ( empirical formula ) are LESS abundant (negative allowed) than the corresponding elements of this EmpiricalFormula
estimateFromWeightAndComp(self, ...)	Fills this EmpiricalFormula with an approximate elemental composition for a given average weight and approximate elemental stoichiometry
estimateFromWeightAndCompAndS(self, ...)	Fills this EmpiricalFormula with an approximate elemental composition for a given average weight, exact number of sulfurs, and approximate elemental stoichiometry
getAverageWeight(self)	Returns the average weight of the formula (includes proton charges)
getCharge(self)	Returns the total charge
getConditionalFragmentIsotopeDist(self, ...)
getElementalComposition(self)	Get elemental composition as a hash {'Symbol' -> NrAtoms}
getIsotopeDistribution	Overload:
getMonoWeight(self)	Returns the mono isotopic weight of the formula (includes proton charges)
getNumberOfAtoms(self)	Returns the total number of atoms
hasElement(self, element)	Returns true if the formula contains the element
isCharged(self)	Returns true if charge is not equal to zero
isEmpty(self)	Returns true if the formula does not contain a element
setCharge(self, charge)	Sets the charge
toString(self)	Returns the formula as a string (charges are not included)

calculateTheoreticalIsotopesNumber(self) → float

contains(self, ef: EmpiricalFormula) → bool

Returns true if all elements from ef ( empirical formula ) are LESS abundant (negative allowed) than the corresponding elements of this EmpiricalFormula

estimateFromWeightAndComp(self, average_weight: float, C: float, H: float, N: float, O: float, S: float, P: float) → bool

Fills this EmpiricalFormula with an approximate elemental composition for a given average weight and approximate elemental stoichiometry

estimateFromWeightAndCompAndS(self, average_weight: float, S: int, C: float, H: float, N: float, O: float, P: float) → bool

Fills this EmpiricalFormula with an approximate elemental composition for a given average weight, exact number of sulfurs, and approximate elemental stoichiometry

getAverageWeight(self) → float

Returns the average weight of the formula (includes proton charges)

getCharge(self) → int

Returns the total charge

getConditionalFragmentIsotopeDist(self, precursor: EmpiricalFormula, precursor_isotopes: Set[int], method: CoarseIsotopePatternGenerator) → IsotopeDistribution

getElementalComposition(self) → Dict[bytes, int]

Get elemental composition as a hash {‘Symbol’ -> NrAtoms}

getIsotopeDistribution()

Overload:

getIsotopeDistribution(self, in_0: CoarseIsotopePatternGenerator) → IsotopeDistribution

Computes the isotope distribution of an empirical formula using the CoarseIsotopePatternGenerator or the FineIsotopePatternGenerator method

Overload:

getIsotopeDistribution(self, in_0: FineIsotopePatternGenerator) → IsotopeDistribution

getMonoWeight(self) → float

Returns the mono isotopic weight of the formula (includes proton charges)

getNumberOfAtoms(self) → int

Returns the total number of atoms

hasElement(self, element: Element) → bool

Returns true if the formula contains the element

isCharged(self) → bool

Returns true if charge is not equal to zero

isEmpty(self) → bool

Returns true if the formula does not contain a element

setCharge(self, charge: int) → None

Sets the charge

toString(self) → bytes | str | String

Returns the formula as a string (charges are not included)