rinchi – An R package to generate InChI’s and InChI Keys

While trying to update rcdk on CRAN it was pointed out to me that usage of the library resulted in modifications to the users home directory. Specifically, this occurred when generating InChI‘s. The CDK makes use of jni-inchi, which in turn depends on JNATI which enables Java code to work with native libraries in a platform […]

Fingerprint Similarity Searches in MongoDB

A few of my recent projects have involved the use of MongoDB, primarily for the ease afforded by a schemaless environment. Sometime back I had investigated the use of MongoDB to store chemical structure data, though those efforts did not actually query structures per se; instead they queried for precomputed numeric or text properties. So […]

Accessing Chemistry on the Web Using Firefox

With the profusion of chemical information on the web – in the form of chemical names, images of structures, specific codes (InChI etc), it’s sometimes very useful to be able to seamlessly retrieve some extra information while browsing a page that contains such entities. The usual way is to copy the InChI/SMILES/CAS/name string and paste […]

Retrieving Target Classifications from ChEMBL

There are a number of scenarios when it’s useful to be able to classify protein targets – high level summaries, enrichment calculations and so on. There are a variety of protein classification schemes out there such as PANTHER, SCOP and InterPro. These schemes are based on domains and other structural features. ChEMBL provides it’s own […]