Re: [Cdk-devel] CDK 2D structure diagram in JavaScript

[Nina J. <jel...@gm...>]

On 2 September 2014 15:11, gilleain torrance <gil...@gm...>
wrote:

> Hi,
>
> Ah, I forgot to cc the mail to your address - I never get the hang of
> that on mailing lists.
>
> Okay, so it's quite a mashup of different technologies then. So two
> options are:
>
> 1) Translate the CDK source with J2S, GWT, or similar.
> 2) Run the CDK as a back-end web service.
>
> For the first one, I spent a bit of time yesterday looking at
> Java->JavaScript translation (or 'transpiling'!) and one thing I
> couldn't work out is how dependencies work. The CDK depends on a
> number of other java libs - such as jgrapht - which would presumably
> have to be also converted to JS.
>
> As for the second, there has been other work in this area.
> Ambit/OpenTox for example (http://ambit.sourceforge.net/index.html,
> http://www.opentox.org) which has web services for various things,
> including 2D layout of molecules. I don't know too much about this
> project, and obviously it does a lot more than you require. A very
> simple servlet that just takes a SMILES and returns some 2D layout as
> (say) a mol file should be easy enough if that's all you need.
>
>
AMBIT has services for all functionality required (and more), and the
recent version (2.5.8 released 31.08 , ambit2.war download at
sourceforge.net ) has integration of ChemDoodle editor (and implementation
of server side  layout and aromaticity as required by ChemDoodle sketcher).

http://apps.ideaconsult.net:8080/data/ui/_search

(try the rightmost button with the pen icon)

These are REST services (CORS could be enabled and you could run the server
and the client JS on different sites).

I'd be glad to answer specific questions.

Regards,
Nina


> Any which way - it's nice to see an exploration of 2D/3D views like
> this. Perhaps a crowdfunded approach to this would be successful.
> Certainly molecular graphics usually look nice enough to get some
> attention!
>
> gilleain
>
> On 9/2/14, Herman Bergwerf <her...@gm...> wrote:
> > About CDK in MolView (http://molview.org)
> >
> > Sorry for the late response, I was not subscribed to the CDK devel
> mailing
> > list so I haven't recievee your replies (until I found them on
> sourceforge)
> >
> > MolView is built on top of GLmol, ChemDoodle Web and JSmol.
> > GLmol is used as primary render engine (fast), ChemDoodle is used for
> > crystals (CIF is not yet implemented in GLmol) and JSmol is used as
> > Canvas2D fallback and for advanced actions like force field minization,
> > dipole calculation and measurements.
> >
> > I've looked at the CDK source but there are a lot of dependencies (eg.
> > other packages in the DiagramGenerator)
> >
> > Can CDK also generate 3D coordinates? (without force field minimization
> but
> > using templates etc.) Because that would be a great alternative to the
> > Chemical Identifier Resolver (
> http://cactus.nci.nih.gov/chemical/structure)
> >
> > Maybe I should use J2S after all...
> > I'm also thinking about a larger server-side part in MolView (but I'll
> need
> > some crowdfunding) Then I could put CDK on a Tomcat server or something
> > like that.
> >
> > Btw, MolView will be made open-source in the future!
> >
>
>
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