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 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.
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.
