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In the fingerprint similarity paper I published last year, I made the following observation: "However the use of the mean rank is itself problematic as the pairwise similarity of two methods can be altered (and even inverted) by adding additional methods to...
Hydrogens are not usually listed explicitly in a SMILES string, but instead can be inferred from a set of rules. To be precise, when reading a SMILES, the position of every hydrogen is known unambiguously once you know the rules. Oh - did I forget to mention...
In earlier posts I discussed/investigated how stereochemistry is represented in SMILES. Here I'm going to try to figure out what I thought would be relatively simple, how to write a SMARTS pattern that matches a chiral molecule and all of its superstructures....

Most popular posts

I've already mentioned using Open Babel for depicting with SVG. That's a handy way to view a large set of molecules; you can zoom in and out and so forth. Let's look at some more of the features, as I've just been adding them to PNG depiction from SVG. Let's...
How cool is SVG? Way, I say. Combine it with some sweet sweet JavaScript (indeed, is there any other kind?) and you can visualise large numbers of molecules with low memory footprint (vectors don't use much memory) even in the tiny 600px margin of this blog...
The image above says it all. We've packaged up the Open Babel user documentation as a book and it's now available for purchase from Lulu at the cost price of 7.48 (since the postage may cost almost as much, you may want to consider buying Egon's and Angel's...

Latest posts linking here

I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle...
A very long time ago, Scalable Vector Graphics promised to revolutionalize images on the web. After initial cool work (including CMLSnap: animated chemical reactions by Peter's group!), things cooled down. There was simply a lack of support in browsers. Things...
The new OpenBabel book acknowledges the contributors to the project (deduced from Jrg's thanx). My Groovy Cheminformatics book is about using the CDK, not about the project itself really, but shows many similarities to the OpenBabel book. Edition 1.3.8-0 of...