Friday, 18 December 2009

Chemical Identifier Resolver + TwirlyMol = Easily add molecules to a webpage II

Noticed anything different about the TwirlyMols over at Carbon-based Curiosities, Chemical Quantum Images, or Node in the Noosphere? (Here's a hint - perhaps they look more awesome?)

Yes, indeed, TwirlyMol now uses proper spherical shading for the atoms. In addition, if you are using any of the 5 or so browsers that are not Internet Explorer (shame on you, IE), you will see that distant atoms are now wreathed in a fog (really it's a representation of the uniform electron gas). Through the magic of the internets, any TwirlyMol using the Chemical Identifier Resolver will suddenly look a whole lot better.

We've also addressed some minor bugs: shadows in wrong place, loading issues with multiple molecules, slow loading, issues with Opera.

Markus has also been doing some work on caching. To take advantage of this new work (and shave several seconds off load times), use the following new HTML:
<div id="DIVNAME" height="200" width="200"></div>

<script src="

Here's an example of it in action, where the CHEMICAL_IDENTIFIER is restasis and the DIVNAME is foggymol:

Wednesday, 16 December 2009

Cheminformatics Tutorial using Python and Silverlight II

Part I

I've updated the Interactive Cheminformatics Tutorial by adding sections on descriptors and molecular fingerprints, and removing the original Python tutorial (following Michael Foord's suggestion). In summary, the tutorial could now form the basis of a course on cheminformatics.

Currently the tutorial focuses on the possibilities of the Cinfony API but a possible improvement would be to include more didactic material, for example describing SMILES strings, their syntax and so forth.

One of the nice things about the Chemical Identifier Resolver is that it allows you to reference molecules by name which really brings a bit more life to the examples. Using this I've tried to think up interesting examples (e.g. "What's the Tanimoto similarity of aspirin to Dr. Scholl's Wart Remover?"). Additional suggestions are very welcome.