I ran across John Bradshaw’s excellent presentation Strings and Things. Part historical overview, part explanation of the SMILES/SMARTS line notation systems, Bradshaw’s slides are chock full of interesting tidbits. My favorite: slide 29 - “Line notations are dead.” It’s a wonderful illustration of why predicting the future of technology is so tricky.

Update: Firefly has since been completed and is now called ChemWriter™. ChemWriter can be downloaded and licensed. The previous article in this series outlined the main technical constraints in the design of Firefly, a new chemical structure editor for the Web. Knowing the technical barriers you’re up against is important in any software project, but understanding what the software needs to do is also important.

A previous article discussing the deployment of four free 2D structure editors has been fixed. The sample pages demonstrating how to obtain a molfile from each have also been restored.

One of the strange things about writing a blog is stumbling on your own work in Google’s search results. In doing some research for a talk, I noticed that Depth-First articles appear at the top of many Google searches. I’m not sure what to make of this, but for what it’s worth, here are some unquoted Google search terms that currently return a Depth-First article in the top-three results: free chemistry databases Number two.

A previous article outlined the major concepts behind Firefly, a new 2D structure editor for the Web. Structure editors are unique in that they require solutions to problems in so many different areas: graphical user interface design; chemical structure aesthetics; 2D graphics and geometry; molecular representation; and graph theory, to name a few.

Of the many cheminformatics technologies developed over the last fifty years, which ones can no bench chemist function without today? There are many possibilities to choose from: molecular databases, fast substructure searching, the SD/Molfile format, SMILES and other line notations, a variety of molecular descriptors and in silico property calculations, and QSAR, to name a few. Throw in molecular modeling and 3-D visualization if you’d like.

Are you thinking of building a free chemical database but would rather not rent and maintain a bunch of proprietary software components?

Given a molecule with no 2D coordinates, how would you render a human-readable view? This problem arises in many situations, but most commonly in the context of interpreting line notations such as IUPAC nomenclature, SMILES, or InChI. Whatever the solution you come up with, you’ll come face-to-face with the structure diagram generation (SDG) problem.

Open Babel 2.1.0 has just been released. Among its new features is a Ruby interface containing most of the functionality of the C++ library. Installation is quick and easy, as shown in this article. Prerequisites In addition to a working build system, you’ll need Ruby and the Ruby development libraries.

Axial chirality isn’t the first thing most chemists come up with when they think of indole. Yet a recent J. Org. Chem. article by Kamikawa et al. describes not only axially chiral indoles, but an enantioselective method for their synthesis. Axial chirality has been largely ignored by the cheminformatics community. There was once a time when the phenomenon was esoteric enough that it could be reasonably ignored.

Unlike many data types, molecular structure representations are not normally unique. Each numbering system you choose for the atoms and bonds of a molecule gives rise to completely accurate, but degenerate molecular representations. This is one of the fundamental peculiarities of chemical information - and the focus of much research activity over the last sixty or so years.