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About four years ago I speculated that JavaScript may be capable of filling some important holes in chemistry software. Since then, a number of important events have taken place to move JavaScript onto center stage as a programming language, including the release of Chrome with its huge JavaScript performance increases and rocket trajectory to overtake IE as the most popular browser, the runaway success of iOS as a computing platform free of browser plugins, the renaissance of server-side JavaScript through Node.js and other frameworks, and a dazzling array of languages like CoffeeScript that compile to JavaScript.

JavaScript for cheminformatics has started to look a lot less improbable as well. In late 2010, my company began distributing the first copies of its chemical structure editor ChemWriter - a complete rewrite of the original Java applet in JavaScript. Following this, we released the plugin- and server-free chemical structure rendering package ChemVector. Other companies now offer products in this space as well, with indications that big players are now starting to take notice.

This article highlights a small part of some work I'm now doing that demonstrates the readiness of JavaScript to solve difficult cheminformatics problems.

Demo: Read a ChemDraw File

Given an arbitrary binary ChemDraw CDX file, it's now possible to print out the encoded object graph in a JavaScript console. For example, this file generates this output:

For background, see previous D-F articles on the ChemDraw CDX file format and the CDX HexDumper utility.

Being able to visualize the contents of arbitrary CDX files this way is an important aid to debugging and a prerequisite to developing full-featured graphical display capability.

Why Read ChemDraw Files in JavaScript?

It's a pretty safe bet that any organic chemist who has written a report, submitted a journal manuscript, or filed a patent has used ChemDraw. As a result, ChemDraw files are everywhere in chemistry.

If you've spent any time watching how chemists work, the need to manipulate CDX files may be obvious. Even so, I'd like to offer a specific example taken from a recent project that illustrates that the need to work with CDX files can come from some unlikely places.

Reagents is iOS Organic Chemistry reference app that I co-developed with James Ashenhurst. It makes heavy use of ChemDraw CDX files to display structures and reaction schemes.

These structures and reactions schemes are automatically pre-rendered through AppleScript automation of the ChemDraw application. Although this works, it's far from optimal. For example, Reagents runs on iPad 3 (retina) displays. To prevent pixellation, our horizontal resolution measures in the thousands of pixels. The large size of the resulting images means more storage space and longer download times. But the biggest problem lies in the fact that every time we make changes to these ChemDraw files, we must regenerate the corresponding raster image.

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It would be so much better to dynamically render these ChemDraw files inside an iOS UI element such as UIWebView.

We'd also like to do interesting things with the ChemDraw files themselves. I won't spill the beans here, but suffice it to say that if we're successful you'll be seeing one or more new iOS apps that repurpose the Reagents content in some interesting ways.

Yet another use case for a pure JavaScript CDX reader and display component would be in interfacing the system clipboard with a paste target in a Web page. ChemWriter currently supports this capability on Windows, but there's much more we could do.

Larger Vision

JavaScript has established a strong foothold in every area of modern computing: tablets; mobile; web browser; and server. But at the same time, there is no full-featured cheminformatics platform, commercial or otherwise, for building chemistry software in JavaScript.

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We have many of the components for such a platform, but they're spread over different products and applications. Having been developed over the course of a couple of years, the code itself show signs of needing a refresher. A unified, well-designed JavaScript platform centralizing core cheminformatics functionality would be a valuable asset in the continued development of useful tools and applications.

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Given the centrality of the CDX file format in chemistry, we're starting there first.