Archive for December, 2008
I met with Jean-Claude Bradley yesterday and we had a pretty useful hack session, allowing him to easily incorporate chemical and cheminformatics functionality into a GoogleDocs spreadsheet.
A common task that Jean-Claude wanted to automate was the calculation of milligrams (or milliliters) of a chemical required for a certain molarity. So what we need for this calculation is the compound name, desired molarity, molecular weight and the density. Importantly, the people who’d like to use this will provide compound names and not a directly parseable SMILES. So we’d also like to (optionally) get the SMILES. Finally, he wanted to be able to do this in a Google spreadsheet – rather than a specific web page or stand alone program.
A while back I wrote about some updates I had made to the CDK fingerprinting code to improve performance. Recently Egon and Jonathan Alvarsson (Uppsala) had made even more improvements. Some of them are simple fixes (making a String final, using Set rather than List) while others are more significant (efficient caching of paths). In combination, they have improved performance by over 50%, compared to my last update. Egon has put up a nice summary of performance runs here. Excellent work guys!