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/rcdk/man/ops.Rd

http://github.com/rajarshi/cdkr
Unknown | 35 lines | 35 code | 0 blank | 0 comment | 0 complexity | 277fc26426936309d5c5e8dca98bb2ca MD5 | raw file
 1\name{do.aromaticity}
 2\alias{do.aromaticity}
 3\alias{do.typing}
 4\alias{do.isotopes}
 5\title{
 6Perform Aromaticity Detection, atom typing or isotopic configuration
 7}
 8\description{
 9These methods can be used to perform aromaticity detection, atom
10typing or isotopic configuration on a molecule object. In general, when molecules are
11loaded via \code{\link{load.molecules}} these are performed by
12default. If molecules are obtained via \code{\link{parse.smiles}}
13these operations are not performed and so the user should call one or
14both of these methods to corrrectly configure a molecule.
15}
16\usage{
17do.aromaticity(molecule)
18do.typing(molecule)
19do.isotopes(molecule)
20}
21\arguments{
22  \item{molecule}{The molecule on which the operation is to be
23  performed. Should of class \code{jobjRef} with a \code{jclass}
24  attribute of \code{IAtomContainer}}
25}
26\value{
27 No return value. If the operations fail an exception is thrown and an
28 error message is printed
29}
30\keyword{programming}
31\seealso{
32  \code{\link{load.molecules}},
33  \code{\link{parse.smiles}}
34}
35\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}