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/rcdk/man/parsesmiles.Rd

http://github.com/rajarshi/cdkr
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 1\name{parse.smiles}
 2\alias{parse.smiles}
 3\title{
 4  Parse a Vector of SMILES Strings
 5}
 6\description{
 7  This function parses a vector of SMILES strings to generate a list of
 8  \code{IAtomContainer} objects. Note that the resultant molecule will
 9  not have any 2D or 3D coordinates.
10
11  Note that the molecules obtained from this method will not have any
12  aromaticity perception, atom typing or isotopic configuration 
13  done on them. This is in
14  contrast to the \link{load.molecules} method. Thus, you should
15  perform these steps manually on the molecules.
16}
17\usage{
18parse.smiles(smiles, kekulise=TRUE)
19}
20\arguments{
21  \item{smiles}{A SMILES string}
22  \item{kekulise}{If set to \code{FALSE} disables electron checking and 
23  allows for parsing of incorrect SMILES. If a SMILES does not parse by default, try
24  setting this to \code{FALSE} - though the resultant molecule may not have consistent
25  bonding. As an example, c4ccc2c(cc1=Nc3ncccc3(Cn12))c4 will not be parsed by default
26  because it is missing a nitrogen. With this argument set to \code{FALSE} it will parse
27  succesfully, but this is a hack to handle an incorrect SMILES}
28}
29\examples{
30smiles <- c('CCC', 'c1ccccc1', 'C(C)(C=O)C(CCNC)C1CC1C(=O)')
31mol <- parse.smiles(smiles[1])
32mols <- parse.smiles(smiles)
33}
34\value{
35  A list of \code{jobjRef}s to their corresponding CDK \code{IAtomContainer} objects. If a
36  SMILES string could not be parsed, \code{NA} is returned instead.
37}
38\keyword{programming}
39\seealso{
40  \code{\link{load.molecules}},
41  \code{\link{get.smiles}},
42  \code{\link{get.smiles.parser}},
43  \code{\link{view.molecule.2d}},
44  \code{\link{do.aromaticity}},
45  \code{\link{do.typing}},
46  \code{\link{do.isotopes}}
47}
48\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}