Can somebody with more experience with the builder provide a code
example?
Begin forwarded message:
> From: Josep Cester Bofarull <josep.ces...@urv.cat>
> Date: December 19, 2008 3:26:29 AM EST
> To: Rajarshi Guha <rg...@indiana.edu>
> Cc: CCL Subscribers <chemis...@ccl.net>
> Subject: Re: CCL: SMILES to VRML or X3D
> Reply-To: josep.ces...@urv.cat
>
> Thank you for your response Rajarshi,
>
> as I did with JOELib2, I've succeeded in build a CML file from an
> SMILES with CDK with this simple code:
>
> ####
> SmilesParser sp = new SmilesParser
> (DefaultChemObjectBuilder.getInstance());
> IMolecule m = sp.parseSmiles("C(=O)(N)N");
> StringWriter output = new StringWriter ( ) ;
> CMLWriter cmlwriter = new CMLWriter ( output ) ; try
> { cmlwriter.write ( m ) ;
> cmlwriter.close ( ) ; } catch
> ( Exception e ) { System.out.println ( e ) ; }
> System.out.println("CML: " + output.toString ( ) );
> ####
>
> The problem I have is that I don't know how to specify 3d
> coordinates in this CML. Could you give me some example of how to
> do this?
>
> Thank you.
>
> Josep
>
> En/na Rajarshi Guha ha escrit:
>>
>> On Dec 18, 2008, at 8:58 AM, Josep Cester josep.cester]![urv.cat
>> wrote:
>>
>>>
>>> Sent to CCL by: "Josep Cester" [josep.cester===urv.cat]
>>> Hello,
>>>
>>> I need to convert SMILES to VRML or X3D in a java application.
>>> Does exists any java library to do it?
>>>
>>> The only way I've found to get an X3D file from an SMILES is
>>> converting SMILES to CML (with OpenBabel) and then apply an XSL
>>> stylesheet to convert CML to X3D. The problem I have is that
>>> OpenBabel is not written in java. I have also tried JOELib2 to
>>> convert SMILES to CML, but the CML I get has not got 3D coordinates.
>>
>> You can use the CDK to go from SMILES to CML
>>
>> -------------------------------------------------------------------
>> Rajarshi Guha <rg...@indiana.edu>
>> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
>> -------------------------------------------------------------------
>> "I'd love to go out with you, but my favorite commercial is on TV."
>>
>>
>>
>
> --
> Josep Cester Bofarull
> FeT - DEQ
> Universitat Rovira i Virgili
-------------------------------------------------------------------
Rajarshi Guha <rg...@indiana.edu>
GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
-------------------------------------------------------------------
My Ethicator machine must have had a built-in moral
compromise spectral phantasmatron! I'm a genius."
-Calvin
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