Hello, Finally I've found the way to get 3D coordinates. I use ModelBuilder3D:
// get 3D cooords mb3d = ModelBuilder3D.getInstance(TemplateHandler3D.getInstance(),"MMFF94");//"MMFF94" IMolecule m = mb3d.generate3DCoordinates(molecule, true); Of course you won't get the real 3D coordinates, since this is found in molecule's mol file, but you'll be able to paint a molecule in 3D. Josep En/na Rajarshi Guha ha escrit: > Can somebody with more experience with the builder provide a code > example? > > Begin forwarded message: > >> From: Josep Cester Bofarull <[email protected]> >> Date: December 19, 2008 3:26:29 AM EST >> To: Rajarshi Guha <[email protected]> >> Cc: CCL Subscribers <[email protected]> >> Subject: Re: CCL: SMILES to VRML or X3D >> Reply-To: [email protected] >> >> 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 <[email protected]> >>> 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 <[email protected]> > 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 > > > -- Josep Cester Bofarull FeT - DEQ Universitat Rovira i Virgili ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
