I’ve just uploaded a new version of the fingerprint package (v3.3) to CRAN that implements some ideas described in Nisius and Bajorath. First, the balance method generates “balanced code” fingerprints, which given an input fingerprint of N bits, returns a new fingerprint of 2N bits, such that the bit density is exactly 50%. Second, bit.importance […]
New Version of rcdk
Based on feedback from the recent R workshop at the EBI, I’ve updated the rcdk package to include more methods operating on atoms, a modification to parse.smiles to allow it to handle a vector of SMILES strings, which makes it more R-like (thanks to Tobias Verbeke for the patch). In addition, one can now load […]
Spreading the Word About R & Cheminformatics
These last few days I’ve been in the UK for an EBI workshop on cheminformatics in R. It was a two day workshop, the first day focusing on general cheminormatics in R using the rcdk and rpubchem packages, and the second day focusing on doing mass spectrometry in R using XCMS and Rdisop, run by […]
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 […]
rcdk On GitHub
I’ve been working on the rcdk and rcdklibs R packages that integrate the CDK into the R environment. For the past year or two it’s been hosted on r-forge.r-project.org which has a nice feature of nightly builds of R packages. Unfortunately their version control system is Subversion. Having used Git for my other projects, this was […]