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/rcdk/man/viewmol2d.Rd

http://github.com/rajarshi/cdkr
Unknown | 81 lines | 75 code | 6 blank | 0 comment | 0 complexity | 0200994f8934db42bf26500da21ddab4 MD5 | raw file
 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})}