You can script the CDK in python using -

There is also:


On 28 Mar 2014, at 05:37, Egon Willighagen <> wrote:

Dear Saulius,

On Thu, Mar 27, 2014 at 1:21 PM, Saulius Gražulis <grazulis@...> wrote:
In addition, CDK, being a library, is not directly usable in
Perl/Shell/Unix environment. Someone some day has to build a set of Unix
executables for CDK to be usable in our context... Like ones you have
build in Vilnius for Jumbo, for instance.

We used to have those, but since they were not used a lot at the time
(years and years ago), we stopped maintaining them.

This weekend, during the #blueobelisk hackathon in Cambridge, we
discussed it again, as there is now a simple framework that takes away
much of the work... I am tempted to introduce the cmd line apps for
the CDK again (in a separate project)...

So, what would you need? Please file needs here:

Another approach would be to try to call CDK directly from the Perl
using Inline::Java module, but then again we need to build objects
suitable for CDK.

Interesting idea... the command line utils I have an idea about how I
would do that... for this, I am not sure, but I can imagine they share
the wrapping "command" classes...


E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (
ORCID: 0000-0001-7542-0286

Cdk-user mailing list