surajit ray wrote:
> Hi Nina,
>
> tried a few ... for example 
>  (with mime type application/rdf+xml)
>
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/3287/conformer/262287
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/17611/conformer/262288
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/3287/conformer/262287
>
> I tried the same with Chemical mime type and got an sdf file ...
>
> However I could not get a SMILE string anywhere in the response ....
> do I have to do something else to get a smile string in a response ?

Have you tried mime type "chemical/x-daylight-smiles"  ?  This will you
give you SMILES string.
>
> Also is there an easy way to get a set of molecules and their smiles.
> This currently looks like I have to first get and iterate over the rdf
> model and then send individual get requests (with chemical mime type)
> to get the SDF file (how to get SMILE - i still dont know ...)
The SDF/MOL itself contains structures, no need of SMILES; if only
SMILES is what you are looking for, use mime type
"chemical/x-daylight-smiles" . I think Christoph is using SMILES as well.

Regards,
Nina
>
> Thanks 
> Surajit
>
> On Sat, Feb 20, 2010 at 1:01 AM, Nina Jeliazkova <nina at acad.bg
> <mailto:nina at acad.bg>> wrote:
>
>
>     >
>     > b) how do I retrieve the value contained in the Feature node in the
>     > statement :
>     >
>     >                 RDFNode value =
>     fv.getProperty(OT.value).getObject();
>     >                 out.write(String.format("%s=%s\n",
>     >                         //Feature
>     >                        
>     fv.getProperty(OT.feature).getObject().toString(),
>     >                         //Value
>     >                         value));
>     >
>     > Value is a string representation of the node like so
>     > : Cc1ccc(N=Nc2c(O)ccc3ccccc23)c(c1)N(=O)O^^
>     > http://www.w3.org/2001/XMLSchema#string
>     >
>     > I would like to retrieve the just the value (the smile string ...)
>     >
>     >
>
>        if (value.isLiteral() )
>           ((Literal) value).getString();
>
>
>     will return the string value; there are similar functions for
>     other data
>     types.   But again, use it for data values, not chemical structures.
>
>     Regards,
>     Nina
>
>
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>
>
> -- 
> Surajit Ray
> Partner
> www.rareindianart.com <http://www.rareindianart.com>