Recently, a question was raised on the Yahoo cheminf group list regarding the conversion of IUPAC names into molecular formulas. This can be done quickly with Ruby CDK, as this article will show. Prerequisites This tutorial requires Ruby CDK, which in turn requires Ruby Java Bridge (RJB). A recent Depth-First article described the minimal system configuration required to run RJB on Linux. Another article showed how to install RJB on Windows.

Whatever happened to chemistry and the Web? Stu Borman’s article is a wonderful read, if for no other reason than to illustrate what makes technology predictions so tricky. Borman cites these developments, among others, as evidence of the rise of chemistry on the Web circa 1996: An AltaVista search for the word “chemistry” returned 400,000 documents. (Remember AltaVista?

FooDB contains over 1,900 structures used as food additives in the United States. The data in FooDB are provided by the FDA EAFUS site. You can search by CAS number, IUPAC name, or molecular formula. And in what is likely to be a trend to watch closely, FooDB is powered by the Web application framework Ruby on Rails. FooDB is not alone: the number of free chemistry databases on the Web just keeps growing.

Wouldn’t it be wonderful if chemical structure searching were as easy as using Google? Draw your molecule, press a button and get the good stuff first. That day may well arrive, but without the creation of some key technologies, the wait will be very long. This article describes an unsuccessful attempt to bring the chemically-aware Web closer to reality. Recently, I introduced a small Web application called InChIMatic.

When building software, the temptation to add nifty but useless features can be very strong. This temptation becomes almost irresistible when a clear vision of the final product is missing. What separates software that people love to use from software that people have to use? In many cases, it’s the discipline to say “no” to feature blight.

Bryan Vickery’s interview is interesting on a number of levels, not the least of which being that it appears in an ACS publication. His comments raise the obvious question of why does the academic/research community continue to support existing publishing models, complaints notwithstanding. The answer to this question is the key to fixing what’s broken.

InChIMatic, as described previously, is a new service that lets you perform exact structure searches on the Web using Google. A new version offers searching via several other search engines and features a streamlined interface. The screenshot below shows the the current search engine options with 1-bromonaphthalene in the editor window. There are noticeable differences in the abilities of search engines other than Google to find InChIs.

Do you remember when getting email - any email - was exciting? For me, that time was 1995 and I had just found the Internet. Of course, I remember looking forward to messages from people I knew. But I also remember being blown away by the idea that I could write to anyone with an email account, anywhere in the world for essentially free - and that they could do the same. Back then, it was fun to get email, no matter what the source.

The number of peer-reviewed publications using the Open Source Java library Chemistry Development Kit (CDK) just keeps growing. The latest addition comes by way of a paper by Fechner and Schneider on ligand-based de novo design. In many areas, Open Source software is used not because it’s free, but because it’s perceived as superior to alternatives. How long will it be before this is true in cheminformatics?

Evan Williams didn’t set out to build Blogger.com - the original product idea for the company he cofounded was an advanced web-based project management tool. Blogger was created on the side as a way for Evan and his cofounder to update their own weblog. The system was eventually made available to the public. Even as the use of this new blogging service took off, Evan remained reluctant to ditch the original project management tool idea.

Peruse the Octet API Documentation and you may find something surprising about the Molecule interface: it lacks mutator methods. Given that mutators enable the state of an object to change, how can a Molecule ever be created in the first place? Why would anyone even need immutable Molecules? Mutable Molecules are Unnecessary Most cheminformatics tools permit the unfettered modification of molecules after their creation.