A few days back, Aaron posted a question regarding the use of the tree width of a graph (intuitively, a measure of how tree like a graph is) in a chemical context. The paper that he pointed to was not very informative in terms of chemical applications. The discussion thread then expanded to asking about […]
Cheminformatics and Hotness (or lack thereof)
A few days back I discussed some thoughts on cheminformatics vis a vis bioinformatics, inspired by a review by Aaron Sterling. In that thread, Steven Salzberg made a comment, stating … In my opinion, it is not a “hot” field, though, in part for some of the reasons mentioned in the post – particularly the […]
Cheminformatics – the New World for TCS?
A few weeks back Aaron Sterling posted a review of the Handbook of Cheminformatics Algorithms (in which I have a chapter). Aaron notes … my goal for the project changed from just a review of a book, to an attempt to build a bridge between theoretical computer science and computational chemistry … The review/bridging was […]
CDK & logP Values
Recently, Tony Williams enquired whether there had been any comparisons of the CDK with other tools for the calculation of polar surface area (PSA) and logP. Given that PSA calculations using the fragments defined by Ertl et al are pretty straightforward, it’s not surprising that the CDK implementation matches very well with the ACD Labs […]
Caching SMARTS Queries
Andrew Dalke recently published a detailed write up on his implementation of the Pubchem fingerprints and provided a pretty thorough comparison with the CDK implementation. He pointed out a number of bugs in the CDK version; but he also noted that performance could be improved by caching parsed SMARTS queries – which are used extensively […]