Parsing SMILES with a frown?

In a recent post, Andrew Dalke compares SMILES parsing in Frowns (a now unsupported Open Source Python cheminformatics library) and the CDK (an actively developed Open Source Java cheminformatics library). Andrew is somewhat of a parsing expert - indeed, BioPython is built upon a parser called Martel which Andrew developed. The Frowns SMILES parser, contributed by Andrew, shows what an expert can do. It would be interesting to know whether similiar code could be incorporated into the CDK and OpenBabel, and if so, what is the speed tradeoff involved?

Andrew also discusses the compression of SMILES strings, which James Melville and Johnathan Hirst have also recently been studying. Rajarshi has also reviewed this work.

CIA on the move

If, like me, you like to keep up to date with CVS or SVN commits from SourceForge via RSS (rather than emails), you are probably tracking commits using CIA. This is a amazing light-weight website created by Micah Dowty.

This post is just to let you know that you should update your bookmarks; CIA has moved from http://cia.navi.cx to http://cia.vc (where 'vc' stands for version control). Over the last few months, the ability to add metadata has been made easier, so that you can jazz up your personal and project websites on CIA with a nice photo or logo too.