The second beta release of MX is now available for download. MX is a library of essential cheminformatics models and routines. It was created with the goal of providing a clean, well-tested platform for chemistry applications. This beta release includes a new binary fingerprinter package that was not ready for release in the first beta.
After having spent some time recently playing around with Jmol, the thought occurs - is there a setting that enables 3D-effect viewing with those colored glassed used with movies? For that matter, which of the free 3D molecule viewers currenly available support it?
The idea of creating a system in which a short sequence of characters can be used in place of a molecular structure traces its roots to the beginnings of modern chemistry. As the Web continues to become the information platform of choice - even in chemistry, the need to communicate molecular information in a Web-ready format increases. InChI Recently, InChI has emerged as a candidate for this position - or more precisely, InChIKey has.
Test-driven development (TDD) is an iterative technique for software development in which a failing test is written before a single line of production code is written. Like any technique, it has its limitations and isn’t applicable in every situation. Nevertheless, TDD is a powerful method to create more robust low-level code and more effective high-level designs. The early days of TDD were not much fun.
Substructure search is a fundamental cheminformatics operation, and an especially important component in chemical structure databases. Although a few algorithms for atom-by-atom comparison of two structures are available, one of the fastest is VF, which is implemented in MX, a lightweight cheminformatics toolkit.
The C&EN blog covers a recent innovation symposium. I generally find high-level discussions about innovation to be not terribly useful because they always seem to skirt the central issue, which I posted as a comment: “You’ll know you’re being innovative if you feel uncomfortable.” That’s the best advice on the subject of innovation I ever got.
[Flash Content Scrubbed] Marcus Hanwell discusses the main features of Avogadro, which is a finalist in the 2009 SourceForge Community Choice Awards.
Open Source Cheminformatics from Rajarshi Guha Rajarshi Guha gives a good overview of the state of the art and challenges.
The master branch of MX now features support for two very important cheminformatics capabilities: Extensible Fingerprints. Lets you fine-tune the performance of your binary path-based fingerprints. Change path depth, number of bits, and the characters used to generate the fingerprints. The default implementation differentiates cycle paths from non-cycle paths, as well as unsaturated from saturated atom types.
