In my previous post, I had asked whether we really need AtomContainerSet and other related specialized container classes as opposed to using parametrized List objects. Gilleain had mentioned some issues that might require these specialized classes. But at this point it’s not clear to me what the intended goal for these classes was. For now, […]
Discussion Topics for the CDK Workshop (from an absentee)
The CDK workshop is coming up at the EBI next week and it’s very frustrating to not be able to attend because of stupid US visa issues. While the workshop is not very long and already has an excellent program, I think it’d be useful to have a discussion on larger and broader issues regarding […]
Circular Fingerprints with the CDK and Clojure
One of the things I’m liking about Clojure is that it can be used as a quick prototyping language, a lot like Python. This is quite handy when playing with the CDK, as I can avoid a lot of the verbosity of Java code. As an example, I put together a very simplistic circular fingerprint […]
Manipulating SMARTS Queries
Yesterday, Andreas Maunz asked a question on the openbabel-discuss list: … a possibility to combine two distinct smarts patterns. Of course, there is the comma OR operator (s1,s2), but I was thinking of a more sophisticated combination, where equal parts of s1 and s2 are “mapped onto each other” in a way such that merely […]
Easy Parallelization With Clojure
As I noted in my previous post, one of the nice features of Clojure is its support for concurrent programming. Now, it provides some fancy features that allow one to write complex parallel programs. I’m certainly no expert on that topic. However, one thing that I do everyday is perform operations on elements of a […]