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/rcdk/man/getsmiles.Rd

http://github.com/rajarshi/cdkr
Unknown | 37 lines | 36 code | 1 blank | 0 comment | 0 complexity | 48ea9caab1b902fd4c121aca70567568 MD5 | raw file
 1\name{get.smiles}
 2\alias{get.smiles}
 3\title{
 4  Get the SMILES for a Molecule
 5}
 6\description{
 7  The function will generate a SMILES representation of an
 8  IAtomContainer object. The default parameters of the CDK SMILES
 9  generator are used. This can mean that for large ring systems the
10  method may fail. See CDK Javadocs for more information
11}
12\usage{
13get.smiles(molecule, type = 'generic', aromatic = FALSE, atomClasses = FALSE)
14}
15\arguments{
16  \item{molecule}{A Java object of class \code{IAtomContainer}}
17  \item{type}{The type of SMILES to output. Possible values are
18  \enumerate{
19  \item generic - non-canonical SMILES string, different atom ordering produces different SMILES. No isotope or stereochemistry encoded.
20  \item unique - canonical SMILES string, different atom ordering produces the same* SMILES. No isotope or stereochemistry encoded.
21  \item isomeric - non-canonical SMILES string, different atom ordering produces different SMILES. Isotope and stereochemistry is encoded.
22  \item absolute - canonical SMILES string, different atom ordering produces the same SMILES. Isotope and stereochemistry is encoded.
23  }}
24  \item{aromatic}{If \code{TRUE} aromatic SMILES are generated. The default is to output Kekule form}
25  \item{atomClasses}{If \code{TRUE} include atom classes.}
26}
27\value{
28  An R character object containing the SMILES
29}
30\examples{
31sp <- get.smiles.parser()
32smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
33mols <- parse.smiles(smiles)
34}
35\keyword{programming}
36
37\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}