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CML Today, Part 2

© Adam Hughes

You can often tell quite a lot about the validity of an idea or product from the efforts of others in the field to incorporate it, in some fashion, into their work. A good example of this in the software industry is the Linux operating system. High-end computer users have been quick to embrace Linux, and the result is that there are many utilities and software programs already on the market or being developed to support or employ the Linux environment. As we'll see in this article, the same type of thing has begun to happen for CML, though on a much smaller scale. Still, this situation bodes well for the future of CML.

It is not uncommon these days to here talk of supporting CML formatting tags for input and output whenever a new chemistry software project is considered. Because of the robust, extensible nature of CML, this is true for applications ranging from Java nomenclature applications to performance-vital simulation codes for use on government supercomputers. The mere fact that CML is a consideration in these design processes means that it has come a long way since its inception in 1995, but, even better, some codes have actually incorporated CML formats into their core.

One such software package is Jmol, a molecule viewer and editor which is freely available, along with source code at http://www.openscience.org/jmol/. Taking advantage of modern object-oriented technology, Jmol is written in Java and is presented as a Swing applet. In addition to letting the scientist visualize simulation results, Jmol can be used to display several useful quantities such as normal modes, bond distances, dipoles, etc. In addition, along with supporting the widely-used but differing formats of the ACES II, ADF, GAMESS, and Gaussian programs, along with PDB files, Jmol also supports CML. This is pretty good company to be keeping if you're a file format type in the computational chemistry world!

Jmol is just one of the newer applications that support CML file formats. Others are being developed everyday, and there are also utilities available which aid those who want to make the switch, such as a converter that marks up a PDB format file with CML tags. Given these promising signs, it appears that CML may be a force in the future.

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