/rcdk/man/viewmol2d.Rd
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1\name{view.molecule.2d} 2\alias{view.molecule.2d} 3\alias{view.image.2d} 4\alias{copy.image.to.clipboard} 5\alias{depict} 6\title{ 7 View and Copy 2D Structure Diagrams 8} 9\description{ 10The CDK is capable of generating 2D structure diagrams. These methods 11allow one to view 2D structure diagrams. Depending on the method called 12a Swing JFrame is displayed which allows resizing of the image or a 13raster image (derived from a PNG byte stream) is is returned, which can 14be viewed using \code{\link{rasterImage}}. It is also possible to copy 15a 2D depiction to the system clipboard, which can then be pasted into 16various external applications. 17} 18\usage{ 19view.molecule.2d(molecule, ncol = 4, cellx = 200, celly = 200) 20view.image.2d(molecule, width = 200, height = 200) 21copy.image.to.clipboard(molecule, width = 200, height = 200) 22} 23\arguments{ 24 \item{molecule}{If a single molecule is to be viewed this should be a 25 reference to a \code{IAtomContainer} object. If multiple molecules 26 are to be viewed this should be a \code{list} of such objects. If a 27 character is specified then it is taken as the name of a file and 28 the molecules are loaded from the file} 29 \item{ncol}{The number of columns if a grid is desired} 30 \item{cellx}{The width of the grid cells} 31 \item{celly}{The height of the grid cells} 32 \item{width}{The width of the image} 33 \item{height}{The height of the image} 34} 35\value{ 36\code{view.molecule.2d} and \code{copy.image.to.ckipboard} do not return anything. 37\code{view.image.2d} returns 38an array of the dimensions height x width x channels, from the original 39PNG version of the 2D depiction. 40} 41\details{ 42 For the case of \code{view.molecule.2d}, if a \code{jobjRef} is passed it should be a reference to an 43 \code{IAtomContainer} object. In case the first argument is of class 44 character it is assumed to be a file and is loaded by the function. 45 46 This function can be used to view a single molecule or multiple 47 molecules. If a \code{list} of molecule objects is supplied the 48 molecules are displayed as a grid of 2D viewers. In case a file is 49 specified, it will display a single molecule or multiple molecules 50 depending on how many molecules are loaded. 51 52 For \code{view.image.2d}, the image can be viewed via \code{\link{rasterImage}}. 53 54 \code{copy.image.to.clipboard} copies the 2D depiction to the system clipboard in 55 PNG format. You can then paste into other applications. 56 57 Due to event handling issues, the depiction will show on OS X, but 58 the window will be unresponsive. Also copying images to the clipboard will not work. 59 As a result, on OS X we make use of a standalone 60 helper that is run via the \code{system} command. Currently, this is supported 61 for the \code{view.molecule.2d} method (for a single molecule) and the 62\code{copy.image.to.clipboard} method. In the future, other view methods will also 63be accessible via this mechanism. While this allows OS X users to view molecules, it is 64slow due to invoking a new process. 65 66 The depictions will work fine (i.e., no need to shell out) on Linux and Windows. 67 } 68\examples{ 69m <- parse.smiles('c1ccccc1C(=O)NC')[[1]] 70\dontrun{ 71img <- view.image.2d(m, 100,100) 72plot(1:10, 1:10, pch=19) 73rasterImage(img, 0,8, 2,10) 74} 75} 76\seealso{ 77 \code{\link{view.table}}, \code{\link{rasterImage}}, \code{link{readPNG}} 78} 79\keyword{programming} 80 81\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}