gistfile1.txt

(Returning after having read the full blog post, and a good part of the review.)

@Aaron, interesting review! I believe you conclude that the algorithms in the book are pretty
basic... sadly, that was deliberate... it's more oriented at showing the casual chemist what
cheminformatics algorithms are about, rather than explaining to cutting-edge algorithms there are
in cheminformatics (...), which would make the book unreadable to the target audience. But in
doing so, we alienated the people we (well, I do) would love to collaborate more with! :(

As was clear from particularly Rajarshi's chapter, there is a large open source cheminformatics
community, who is very open (at least I am!) to collaboration, and within the CDK we actually have
such in the past.

One more exciting problem in chemistry you may find attractive, is the enumeration or even
counting of possible graphs given a number of atoms and bonds (vertices and edges). Now, a
chemical graph is a colored graph, and not all edges are allowed. Moreover, we are only interested
in graphs that are non-symmetrical.

Outstanding problems here are to calculate the number of chemical graphs given a number of atoms
(as in a molecular formula, like C4H10O) without enumerating all structures.

Secondly, 'we' would love an open source implementation of an efficient algorithm to enumerate all
chemical graphs. The efficiency here relies primarily in not calculating solutions for which there
already has been calculated a different solution, which happens to be symmetrical equivalent.

Now, this problem has been solved in the proprietary Molgen software, but may provide you with the
right amount of complexity you are looking for.