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

In sneumann/Rdisop: Decomposition of Isotopic Patterns

Calculate mass and isotope information for a molecule given as sum formula

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)

getIsotope(molecule, index)

getFormula(molecule)

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 for the resulting molecule.
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() will parse the sum formula and calculate the theoretical exact monoisotopic mass and the isotope distribution. For a given element, return the different mass values. Since of version 1-65-3, if a charge is specified, the exact mass of the molecule will be reduced or increased by n-times the electron mass (depending on the sign). Also, isotopic masses will additionally be devided by the charge specified to reflect what would be measured in HR-MS.

Value

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.

Author(s)

Steffen Neumann <[e-mail]>

References

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

Examples

# Ethanol
getMolecule("C2H6O")

sneumann/Rdisop documentation built on Oct. 19, 2024, 2:39 p.m.