# So much to do, so little time

Trying to squeeze sense out of chemical data

## Visualizing PAINS SMARTS

A few days ago I had made available a SMARTS version of the PAINS substructural filters, that were converted using CACTVS from the original SLN patterns. I had mentioned that the SMARTSViewer application was a handy way to visualize the complex SMARTS patterns. Matthias Rarey let me know that his student had converted all the SMARTS to SMARTSViewer depictions and made them available as a PDF. Given the complexity of many of the PAINS patterns, these depictions are a very nice way to get a quick idea of what is supposed to match.

(FWIW, the SMARTS don’t reproduce the matches obtained using the original SLN’s – but hopefully the depictions will help anybody who’d like to try and fix the SMARTS).

Written by Rajarshi Guha

December 2nd, 2010 at 1:18 am

Posted in software,cheminformatics

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## Inserting 2D Depictions into R Plots

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:

 1234567891011121314 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 software,cheminformatics

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## 2D Depictions in R Plots

In preparation for the upcoming R workshop at the EBI, I’ve been cleaning up the rcdk package and updating some features. One of the new features is the ability to get a 2D depiction as a raster image. Uptil now, 2D depictions were drawn in a Swing window – this allowed you to resize the window but not much else. You really couldn’t use it for anything else but viewing.

However, R-2.11.0 provides a new function called rasterImage, which overlays a raster image onto a pre-existing plot. It turns out that the png package lets me easily create such a raster image, either from a PNG file or from a vector of bytes. Given a molecules, we can get the byte array of its PNG representation via the view.image.2d function in the latest rcdk. As a result, you can now make a plot and then overlay a 2D depiction within the plot area. For example to get the picture shown alongside, we could do:

 12345 library(rcdk) m <- parse.smiles("C1CC2CC1C(=O)NC2") img <- view.image.2d(m, 200,200) plot(1:10, pch=19) rasterImage(img, 2,6, 6,10)

The latest version of rcdk and rpubchem is not on CRAN yet, but you can get source packages for OS X & Linux and binary packages for Windows at http://rguha.net/rcdk. Note that the latest version of rcdk requires R-2.11.0 along with rJava, rcdklibs, fingerprint and png as dependencies. If you’re interested in contributing check out the git repository.

Written by Rajarshi Guha

May 3rd, 2010 at 9:22 pm

## Improved CDK Depiction Service

The folks at the EBI have been doing some great work on the CDK. A major effort is underway to revamp JChemPaint and part of this involves improving the rendering of 2D depictions. While not complete I rebuilt a version of the CDK 1.2.x branch with the latest rendering code from the jchempaint-primary branch and updated the CDK web service. The results are much nicer, though there’s scope for improvements. See for example

http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1
http://rguha.ath.cx/~rguha/cicc/rest/depict/C1CCCCC12CCCCC2
http://rguha.ath.cx/~rguha/cicc/rest/depict/CC(=O)OC1=CC=CC=C1C(=O)O
http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1CC=CC%23N

Thanks to Gilleain and Egon for pointing me in the right direction. Anybody using this service should see the new depictions automatically

Written by Rajarshi Guha

January 14th, 2009 at 6:04 pm

Posted in Uncategorized,software

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