The CDK is capable of generating 2D structure diagrams. These methods
allow one to view 2D structure diagrams. Depending on the method called
a Swing JFrame is displayed which allows resizing of the image or a
raster image (derived from a PNG byte stream) is is returned, which can
be viewed using rasterImage. It is also possible to copy
a 2D depiction to the system clipboard, which can then be pasted into
various external applications.
get.depictor(width = 200, height = 200, zoom = 1.3, style = "cow",
annotate = "off", abbr = "on", suppressh = TRUE,
showTitle = FALSE, smaLimit = 100, sma = NULL)
view.molecule.2d(molecule, ncol = 4, width = 200, height = 200, depictor = NULL)
view.image.2d(molecule, depictor = NULL)
copy.image.to.clipboard(molecule, depictor = NULL)If a single molecule is to be viewed this should be a
reference to a IAtomContainer object. If multiple molecules
are to be viewed this should be a list of such objects. If a
character is specified then it is taken as the name of a file and
the molecules are loaded from the file
A depiction object. If NULL then one with default settings is created
The number of columns if a grid is desired
The width of the image
The height of the image
Zoom factor
Depiction style. Possible values are 'cow', 'bow', 'wob', 'cob', 'nob'
Annotation style. By default no annotations are added. Possible values include 'number', 'mapidx', 'atomvalue', 'colmap'
Abbreviation style for functional groups. Possible values are 'groups', 'reagents', 'on'
When TRUE show H's otherwise hide them
When TRUE display title
How many SMARTS patterns should be highlighted?
A string containing the SMARTS pattern to match
get.depictor returns a depiction object that can be supplied to other methods.
view.molecule.2d and copy.image.to.ckipboard do not return anything.
view.image.2d returns an array of the dimensions height x width x channels, from the original
PNG version of the 2D depiction.
For the case of view.molecule.2d, if a jobjRef is passed it should be a reference to an
IAtomContainer object. In case the first argument is of class
character it is assumed to be a file and is loaded by the function.
This function can be used to view a single molecule or multiple
molecules. If a list of molecule objects is supplied the
molecules are displayed as a grid of 2D viewers. In case a file is
specified, it will display a single molecule or multiple molecules
depending on how many molecules are loaded.
For view.image.2d, the image can be viewed via rasterImage.
copy.image.to.clipboard copies the 2D depiction to the system clipboard in
PNG format. You can then paste into other applications.
Due to event handling issues, the depiction will show on OS X, but
the window will be unresponsive. Also copying images to the clipboard will not work.
As a result, on OS X we make use of a standalone
helper that is run via the system command. Currently, this is supported
for the view.molecule.2d method (for a single molecule) and the
copy.image.to.clipboard method. In the future, other view methods will also
be accessible via this mechanism. While this allows OS X users to view molecules, it is
slow due to invoking a new process.
The depictions will work fine (i.e., no need to shell out) on Linux and Windows.
# NOT RUN {
m <- parse.smiles('c1ccccc1C(=O)NC')[[1]]
# }
# NOT RUN {
dep <- get.depictor(width=200, height=200)
img <- view.image.2d(m, dep)
plot(1:10, 1:10, pch=19)
rasterImage(img, 0,8, 2,10)
dep$setHeight(as.integer(400))
dep$setWidth(as.integer(400))
copy.image.to.clipboard(m,d) ## Paste into Word
# }
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