Sometime back I was bored and thought that learning Lisp would be a good past time (maybe I should get a life?). I started of with SBCL and then discovered Clojure, a Lisp dialect that compiles to the JVM. The nice thing about this is that it allows one to write Lisp but also interact […]
Cheminformatics in R – rcdk
Being an R aficionado, I do the bulk of my work in R and having grown up with Emacs I tend to dislike having to exit my environment to do “other” stuff. This was the motivation for integrating R and the CDK, so that I could access and manipulate chemical information from within my R […]
Faster Maximum Common Substructures
Recently Syed Asad Rahman of the EBI sent around a message regarding some new code that he has been developing to perform maximum common substructure detection. It employs the CDK but also includes some alternative methods, which allow it to handle some cases for which the CDK takes forever. An example is determining the MCSS […]
Deploying Predictive Models
Over the past few days I’ve been developing some predictive models in R, for the solubility data being generated as part of the ONS Solubility Challenge. As I develop the models I put up a brief summary of the results on the wiki. In the end however, we’d like to use these models to predict […]
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 […]