Editable and Searchable 2D Molecular Images

July 30, 2007

Word processing replaced the typewriter for the simple reason that documents could be prepared and edited so much more quickly. If Web authoring replaces conventional word processors, it will be for the simple reason that Web documents can be found, distributed, reprocessed, and combined with other content so much more effectively. The peculiar nature of chemical structure information complicates chemistry's transition to Web authoring. This article, the first in a series, discusses some of the challenges that lie ahead.

State of the Art: Word/ChemDraw

Microsoft Word allows 2D molecular graphics, typically created with ChemDraw, to be embedded in documents and later edited. Those images can then be copied into Power Point presentations and reused in a variety of other Windows-specific products. This practice has become so widespread throughout industry and academics, that few chemists even think about the technology that many of them rely on several times a week.

Chemical Structures are Peculiar

A 2D molecular image, like the one depicting fluoxetine at the top of this article, is a peculiar beast. On one level, it's a picture that anybody can look at. But on another level, it's a type of object for which manipulation by humans and computers is extremely useful. The combination of Microsoft Word and ChemDraw lets chemists conveniently manage the dual nature of chemical structures.

Live Molecular Images

Why would anybody want to create editable and searchable 2D molecular graphics such as JPGs, PNGs, and SVGs? Alas, technology has a way of moving on just when we're getting comfortable with it (an especially difficult concept for typewriter manufacturers who went bust during the 1980s, and the dedicated word processor manufacturers who followed).

Consider the number of Word and PowerPoint documents you read last week compared to the number of Web pages. Chances are the ratio is at least 1:10. The trend shows no signs of reversing itself.

Although Web authoring tools have been very slow to reach the average user, the blogging explosion has led to rapid evolution in the field. As tools like WordPress, Movable Type, and even Wikipedia race to satisfy the needs of power authors, the average user will rather unexpectedly discover that they have access to perfectly capable tools that let them abandon their over-engineered (and expensive) word processors to experiment with Web publishing.

The Wikipedia Chemisty/Structure Drawing Workgroup hints at what lies ahead for chemistry. Two tools, GChemPaint and ACD ChemSketch, now enable molecular structure information to be embedded in images.

As chemistry turns to the Web as its primary publication medium, chemists will need the same ability to deal with chemical structures offered by their current tools of choice. In articles to follow, I'll discuss some ways this could happen.