Re: [Cdk-devel] JNI-InChI Integration Status

[richard a. <ric...@ya...>]

Hello Sam,

Yes, I've had a chance to work with it - very nice
work.

The JavaDoc for InChIGenerator mentions that:

"Spin multiplicities and some aspects of
stereochemistry are not currently handled completely."

Can you elaborate on the aspects of stereochemistry
not yet handled? What would be some examples of
molecules for which incomplete InChIs would be
generated?


--- Sam Adams <se...@ca...> wrote:

> 
> Hi Egon, Rich,
> 
> Sorry for taking so long to reply - have only just
> been catching up with 
> the CDK list.
> 
> JNI-InChI is purely a JNI wrapper for IUPAC's InChI
> library.
> 
> The InChIGenerator class takes a CDK Atom Container,
> converts it to the 
> InChI library's model, and then uses the InChI
> library to generate an 
> InChI string.
> 
> The InChIToStructure class takes an InChI string,
> uses the InChI library 
> to generate a chemical model, and then generates a
> CDK Atom Container 
> from that.
> 
> There are code examples in the CDK javadoc, and
> junit tests. The 
> JNI-InChI library is itself also well unit tested.
> 
> If you've got any questions, I'll do my best to
> answer.
> 
> Sam
> 
> 
> Egon Willighagen wrote:
> > Sam, might you comment too, please?
> > 
> > On 10/7/07, richard apodaca
> <ric...@ya...> wrote:
> >> Could anyone tell me the status of CDK
> integration
> >> with the jni-inchi library:
> >>
> >> http://jni-inchi.sourceforge.net/
> > 
> > There are unit tests:
> > 
> >
>
http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-inchi.html
> > 
> >> This library looks very promising. Is it
> currently
> >> possible, for example, to convert SMILES->InChI
> or
> >> molfile->InChI with it using CDK?
> > 
> > Yes. It also converts InChI's back into a CDK
> model, but not sure if
> > it is using Ninja for that.
> > 
> > Egon
> > 
> 
> --
> Unilever Centre for Molecular Science Informatics
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> email: se...@ca...
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> 
> 
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___________________________________

Richard L. Apodaca

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