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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/atoms.R
\docType{package}
\name{Atoms}
\alias{Atoms}
\title{Operations on Atoms}
\description{
\code{\link{get.symbol}} returns the chemical symbol for an atom
\code{\link{get.point3d}} returns the 3D coordinates of the atom
\code{\link{get.point2d}} returns the 2D coordinates of the atom
\code{\link{get.atomic.number}} returns the atomic number of the atom
\code{\link{get.hydrogen.count}} returns the number of implicit H’s on the atom.
Depending on where the molecule was read from this may be \code{NULL}
or an integer greater than or equal to \code{0}
\code{\link{get.charge}} returns the partial charge on the atom. If charges
have not been set the return value is \code{NULL}, otherwise
the appropriate charge.
\code{\link{get.formal.charge}} returns the formal charge on the atom. By
default the formal charge will be \code{0} (i.e., \code{NULL}
is never returned)
\code{\link{is.aromatic}} returns \code{TRUE} if the atom is aromatic,
\code{FALSE} otherwise
\code{\link{is.aliphatic}} returns \code{TRUE} if the atom is part of an
aliphatic chain, \code{FALSE} otherwise
\code{\link{is.in.ring}} returns \code{TRUE} if the atom is in a ring,
\code{FALSE} otherwise
\code{\link{get.atom.index}} eturns the index of the atom in the molecule
(starting from \code{0})
\code{\link{get.connected.atoms}} returns a list of atoms that are connected to the specified atom
}
\section{Usage}{
get.symbol(atom)
get.point3d(atom)
get.point2d(atom)
get.atomic.number(atom)
get.hydrogen.count(atom)
get.charge(atom)
get.formal.charge(atom)
get.connected.atoms(atom, mol)
get.atom.index(atom, mol)
is.aromatic(atom)
is.aliphatic(atom)
is.in.ring(atom)
set.atom.types(mol)
}
\section{Arguments}{
atom A jobjRef representing an IAtom object
mol A jobjRef representing an IAtomContainer object
}
\section{Value}{
In the case of \code{\link{get.point3d}} the return value is a 3-element vector
containing the X, Y and Z co-ordinates of the atom. If the atom does not
have 3D coordinates, it returns a vector of the form \code{c(NA,NA,NA)}.
Similarly for \code{\link{get.point2d}}, in which case the return vector is of
length \code{2}.
}
\author{
Rajarshi Guha (\email{rajarshi.guha@gmail.com})
}
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