getMolecule: Calculate mass and isotope information for a molecule given...

In Rdisop: Decomposition of Isotopic Patterns

Description

Parse the sum formula and calculate the theoretical exact mass and the isotope distribution.

Usage

getMolecule(formula, elements = NULL, z = 0, maxisotopes = 10)
getMass(molecule)
getFormula(molecule)
getIsotope(molecule, index)
getScore(molecule)
getValid(molecule)

Arguments

formula	Sum formula
elements	list of allowed chemical elements, defaults to full periodic system of elements
z	charge z of molecule for exact mass calculation
maxisotopes	maximum number of isotopes shown in the resulting molecules
molecule	an initialized molecule as returned by getMolecule() or the decomposeMass() and decomposeIsotope() functions
index	return the n-th isotope mass/abundance pair of the molecule

Details

getMolecule() Parse the sum formula and calculate the theoretical exact monoisotopic mass and the isotope distribution. For a given element, return the different mass values.

Value

getMolecule: A list with the elements

formula	repeated sum formula
mass	exact monoisotopic mass of molecule
score	probability, for given molecules a dummy value which is always 1.0
valid	result of neutrogen rule check
isotopes	a list of isotopes

getMass, getFormula and getScore: return the mass of the molecule as string or real value

Author(s)

Steffen Neumann <[e-mail]>

References

For a description of the underlying IMS see: see citation("Rdisop")

Examples

# For Ethanol:
getMolecule("C2H6O")

Example output

Loading required package: RcppClassic
$formula
[1] "C2H6O"

$score
[1] 1

$exactmass
[1] 46.04186

$charge
[1] 0

$parity
[1] "e"

$valid
[1] "Valid"

$DBE
[1] 0

$isotopes
$isotopes[[1]]
           [,1]        [,2]        [,3]         [,4]         [,5]         [,6]
[1,] 46.0418648 47.04534542 48.04631711 4.904960e+01 5.005324e+01 5.105929e+01
[2,]  0.9749152  0.02293559  0.00210353 4.540559e-05 2.816635e-07 2.324709e-10
             [,7]         [,8]         [,9]        [,10]
[1,] 5.206548e+01 5.307171e+01 5.407796e+01 5.508422e+01
[2,] 8.458096e-14 1.665930e-17 1.857005e-21 1.107409e-25

Rdisop documentation built on Nov. 8, 2020, 5:40 p.m.