So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘rcdk’ tag

Updated version of rcdk (3.2.3)

with 2 comments

I’ve pushed updates to the rcdklibs and rcdk packages that support cheminformatics in R using the CDK. The new versions employ the latest CDK master, which as Egon pointed out  has significantly fewer bugs, and thanks to Jon, improved performance. New additions to the package include support for the LINGO and Signature fingerprinters (you’ll need the latest version of fingerprint).

Written by Rajarshi Guha

October 6th, 2013 at 11:17 pm

Posted in cheminformatics,software

Tagged with ,

Inserting 2D Depictions into R Plots

without comments

Recent versions of rcdk allow you to insert images of chemical structures into R plots, via the view.image.2d and rasterImage functions. One problem with the latter function is that the 2D structure image must be located in plot units, rather than pixel units. Paul Murrell suggested an easy way to insert the raster image into the plot region, maintaining the  native resolution of the image:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
library(rcdk)
m <- parse.smiles("O=C(C1=CC=CC=C1)C1=CC=CC=C1")[[1]]
img <- view.image.2d(m, 200,200)
plot(10:1, pch=19)

## Position the depiction at the lower left corner
dpi <- (par("cra")/par("cin"))[1]
usr <- par("usr")
xl <- usr[1]
yb <- usr[3]
xr <- xl + xinch(200/dpi)
yt <- yb + yinch(200/dpi)

rasterImage(img, xl,yb, xr,yt)

Written by Rajarshi Guha

November 20th, 2010 at 5:09 pm

Posted in cheminformatics,software

Tagged with , ,