Hi Egon,
Maybe you can give that talk online sometime as part of a BBB conference.
Hint hint.
Regarding the Python stuff....
(1) There's no numpy port to Jython. So to access the CDK and numpy at the
same time you need to use CPython+JPype. Cinfony has this all set up for
the user, but just see the start of
https://github.com/cinfony/cinfony/blob/master/cinfony/cdk.py if someone
wants to do it him/herself.
(2) How is Open Babel accessed from Java or Jython? From the point of view
of the user there's a jar file which they just import, and a JNI library
they need to System.loadLibrary. Behind the scenes, the JNI library
connects to the Open Babel C++ library (libopenbabel.so, or
libopenbabel.dll). All of this was enabled with SWIG. Again, Cinfony
simplifies all of this. See the code at the start of
https://github.com/cinfony/cinfony/blob/master/cinfony/pybel.py
HTH,
Noel
On 26 April 2012 08:48, Egon Willighagen <[email protected]> wrote:
> Hi Noel,
>
> I plugged the CDK in the Dutch bioinformatics community at the
> NBIC2012 conference [0]... good feedback, and also people asking about
> Python support, and I had Cinfony on my slides anyway...
>
> Now, people were wondering about Jython (which they typically knew
> about) and C(++) libraries... You do that with OpenBabel... how does
> that work? And, could you use Cinfony to use the CDK and numpy at the
> same time?
>
> Looking forward to hearing from you,
>
> Egon
>
> 0.
> http://chem-bla-ics.blogspot.com/2012/04/my-nbic2012-slides-on-cdk-in-nl.html
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
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