EmpiricalFormula

class pyopenms.EmpiricalFormula

Bases: object

Cython implementation of _EmpiricalFormula

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1EmpiricalFormula.html

__init__()

Cython signature: void EmpiricalFormula() Representation of an empirical formula
Cython signature: void EmpiricalFormula(EmpiricalFormula &)
Cython signature: void EmpiricalFormula(String) EmpiricalFormula Constructor from string
Cython signature: void EmpiricalFormula(ptrdiff_t number, Element * element, ptrdiff_t charge) EmpiricalFormula Constructor with element pointer and number

Methods

`__init__`	Cython signature: void EmpiricalFormula()
`calculateTheoreticalIsotopesNumber`	Cython signature: double calculateTheoreticalIsotopesNumber()
`contains`	Cython signature: bool contains(EmpiricalFormula ef) Returns true if all elements from ef ( empirical formula ) are LESS abundant (negative allowed) than the corresponding elements of this EmpiricalFormula
`estimateFromWeightAndComp`	Cython signature: bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P) Fills this EmpiricalFormula with an approximate elemental composition for a given average weight and approximate elemental stoichiometry
`estimateFromWeightAndCompAndS`	Cython signature: bool estimateFromWeightAndCompAndS(double average_weight, unsigned int S, double C, double H, double N, double O, double P) Fills this EmpiricalFormula with an approximate elemental composition for a given average weight, exact number of sulfurs, and approximate elemental stoichiometry
`getAverageWeight`	Cython signature: double getAverageWeight() Returns the average weight of the formula (includes proton charges)
`getCharge`	Cython signature: ptrdiff_t getCharge() Returns the total charge
`getConditionalFragmentIsotopeDist`	Cython signature: IsotopeDistribution getConditionalFragmentIsotopeDist(EmpiricalFormula & precursor, libcpp_set[unsigned int] & precursor_isotopes, CoarseIsotopePatternGenerator method)
`getElementalComposition`	Cython signature: libcpp_map[libcpp_string,int] getElementalComposition() Get elemental composition as a hash {'Symbol' -> NrAtoms}
`getIsotopeDistribution`	Cython signature: IsotopeDistribution getIsotopeDistribution(CoarseIsotopePatternGenerator)
`getMonoWeight`	Cython signature: double getMonoWeight() Returns the mono isotopic weight of the formula (includes proton charges)
`getNumberOfAtoms`	Cython signature: size_t getNumberOfAtoms() Returns the total number of atoms
`hasElement`	Cython signature: bool hasElement(Element * element) Returns true if the formula contains the element
`isCharged`	Cython signature: bool isCharged() Returns true if charge is not equal to zero
`isEmpty`	Cython signature: bool isEmpty() Returns true if the formula does not contain a element
`setCharge`	Cython signature: void setCharge(ptrdiff_t charge) Sets the charge
`toString`	Cython signature: String toString() Returns the formula as a string (charges are not included)

calculateTheoreticalIsotopesNumber(): Cython signature: double calculateTheoreticalIsotopesNumber()

contains(): Cython signature: bool contains(EmpiricalFormula ef) Returns true if all elements from ef ( empirical formula ) are LESS abundant (negative allowed) than the corresponding elements of this EmpiricalFormula

estimateFromWeightAndComp(): Cython signature: bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P) Fills this EmpiricalFormula with an approximate elemental composition for a given average weight and approximate elemental stoichiometry

estimateFromWeightAndCompAndS(): Cython signature: bool estimateFromWeightAndCompAndS(double average_weight, unsigned int S, double C, double H, double N, double O, double P) Fills this EmpiricalFormula with an approximate elemental composition for a given average weight, exact number of sulfurs, and approximate elemental stoichiometry

getAverageWeight(): Cython signature: double getAverageWeight() Returns the average weight of the formula (includes proton charges)

getCharge(): Cython signature: ptrdiff_t getCharge() Returns the total charge

getConditionalFragmentIsotopeDist(): Cython signature: IsotopeDistribution getConditionalFragmentIsotopeDist(EmpiricalFormula & precursor, libcpp_set[unsigned int] & precursor_isotopes, CoarseIsotopePatternGenerator method)

getElementalComposition(): Cython signature: libcpp_map[libcpp_string,int] getElementalComposition() Get elemental composition as a hash {‘Symbol’ -> NrAtoms}

getIsotopeDistribution()

Cython signature: IsotopeDistribution getIsotopeDistribution(CoarseIsotopePatternGenerator) Computes the isotope distribution of an empirical formula using the CoarseIsotopePatternGenerator or the FineIsotopePatternGenerator method
Cython signature: IsotopeDistribution getIsotopeDistribution(FineIsotopePatternGenerator)

getMonoWeight(): Cython signature: double getMonoWeight() Returns the mono isotopic weight of the formula (includes proton charges)

getNumberOfAtoms(): Cython signature: size_t getNumberOfAtoms() Returns the total number of atoms

hasElement(): Cython signature: bool hasElement(Element * element) Returns true if the formula contains the element

isCharged(): Cython signature: bool isCharged() Returns true if charge is not equal to zero

isEmpty(): Cython signature: bool isEmpty() Returns true if the formula does not contain a element

setCharge(): Cython signature: void setCharge(ptrdiff_t charge) Sets the charge

toString(): Cython signature: String toString() Returns the formula as a string (charges are not included)