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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/molecule.R
\name{Molecule}
\alias{Molecule}
\title{Operations on molecules}
\description{
Various functions to perform operations on molecules.
\code{\link{get.exact.mass}} returns the exact mass of a molecule
\code{\link{get.natural.mass}} returns the natural exact mass of a molecule
\code{\link{convert.implicit.to.explicit}} converts implicit hydrogens to
explicit hydrogens. This function does not return any value but rather
modifies the molecule object passed to it
\code{\link{is.neutral}} returns \code{TRUE} if all atoms in the molecule have
a formal charge of \code{0}, otherwise \code{FALSE}
}
\details{
In some cases, a molecule may not have any hydrogens (such as when read in
from an MDL MOLfile that did not have hydrogens). In such cases,
\code{\link{convert.implicit.to.explicit}} will add implicit hydrogens and
then convert them to explicit ones. In addition, for such cases, make sure
that the molecule has been typed beforehand.
}
\section{Usage}{
get.exact.mass(mol)
get.natural.mass(mol)
convert.implicit.to.explicit(mol)
is.neutral(mol)
}
\section{Arguments}{
mol A jobjRef representing an IAtomContainer or IMolecule object
}
\section{Value}{
\code{\link{get.exact.mass}} returns a numeric
\code{\link{get.natural.mass}} returns a numeric
\code{\link{convert.implicit.to.explicit}} has no return value
\code{\link{is.neutral}} returns a boolean.
}
\seealso{
\code{\link{get.atoms}}, \code{\link{set.atom.types}}
}
\author{
Rajarshi Guha (\email{rajarshi.guha@gmail.com})
}
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