\HeaderA{getMolecule}{Calculate mass and isotope information for a molecule given as sum formula}{getMolecule}
\aliasA{getFormula}{getMolecule}{getFormula}
\aliasA{getIsotope}{getMolecule}{getIsotope}
\aliasA{getMass}{getMolecule}{getMass}
\aliasA{getScore}{getMolecule}{getScore}
\aliasA{getValid}{getMolecule}{getValid}
\keyword{methods}{getMolecule}
\begin{Description}\relax
Parse the sum formula and calculate the theoretical exact mass and
the isotope distribution.
\end{Description}
\begin{Usage}
\begin{verbatim}
getMolecule(formula, elements = NULL, z = 0)
getMass(molecule)
getFormula(molecule)
getIsotope(molecule, index)
getScore(molecule)
getValid(molecule)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{formula}] Sum formula
\item[\code{elements}] list of allowed chemical elements, defaults to full
periodic system of elements
\item[\code{z}] charge z of molecule for exact mass calculation
\item[\code{molecule}] an initialized molecule as returned by
getMolecule() or the decomposeMass() and decomposeIsotope() functions
\item[\code{index}] return the n-th isotope mass/abundance pair of the molecule
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
getMolecule() Parse the sum formula and calculate the theoretical
exact mass and
the isotope distribution. For a given element, return the different
mass values.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{getMolecule}] A list with the elements
\item[formula] repeated sum formula

\item[mass] exact mass of molecule


\item[score] probability, for given molecules a dummy value which is always 1.0


\item[valid] result of neutrogen rule check


\item[isotopes] a list of isotopes 


\item[\code{getMass, getFormula and getScore}] return the mass of the
molecule as string or real value
\end{ldescription}
\end{Value}
\begin{Author}\relax
Steffen Neumann <sneumann@IPB-Halle.DE>
\end{Author}
\begin{References}\relax
For a description of the underlying IMS see:
WABI Paper
\end{References}
\begin{Examples}
\begin{ExampleCode}
# For Ethanol:
getMolecule("C2H6O")
\end{ExampleCode}
\end{Examples}

