On Wed, Apr 24, 2013 at 9:13 AM, Stefan Hoeck <efascken...@gmail.com> wrote:
> Dear all
>
> I am an organic chemist at the Zurich University of Applied Sciences. A
> couple of months ago we published an article in the Journal of
> Cheminformatics about the beginnings of a purely functional cheminformatics
> toolkit written in Scala (the article can be found here:
> http://www.jcheminf.com/content/4/1/38/abstract). So far, this toolkit
> only supports SMILES parsing and representing molecules in a basic,
> immutable graph data structure. I am now looking for people interested in
> pushing this project forward. The toolkit, which we called 'chemf', is
> open-source (the source code is hosted on github:
> https://github.com/stefan-hoeck/chemf) but it hasn't seen much activity
> lately since so far I have been the only person working on it.
>
I am very interested in developing a Scala engine for CML - probably a cut
down version from the complete JUMBO6 . DaveMR (copied) has created a Scala
engine for MathML to integrate maths with chemistry.
>
> So, I am looking for people helping me implement the typical algorithms
> needeam d for a fully fledged cheminformatics toolkit in a purely
> functional, referentially transparent way. The algorithms may be
> implemented in an imperative style in the background, but they need to be
> designed to work with immutable data structures and produce such data
> structures as output. I am aware that there are already quite a few
> cheminformtaics toolkits out there, but to the best of my knowledge, those
> rich in functionality like CDK or Open Babel provide algorithms that
> require mutable data structures to work properly.
>
JUMBO has a wide range of tests so it should be possible to use them to
test the scala engine.
>
> Note, that people wishing to contribute to this project do not necessarily
> need to be able to write Scala code since if one sticks to Scala's
> imperative side, Java source code can typically be transferred to Scala
> source code quite easily.
>
It will be very interesting to see how this works.
>
> Please excuse if this is not the right way or place to address the Blue
> Obelisk community with such a request. Any help or input on this matter is
> highly appreciated.
>
> Absolutely the right place!
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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