Hi!
I solved the problem of displaying molecules come from a smiles. I needed to
use the StructureDiagramGenerator (as I saw here:
http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws.html#sd
g) to generate coordenates of the molecule. So, my application run correctly
!
The code I`ve added is this:
public static Molecule smilesToStructure(String smiles){
SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
Molecule m = null;
Molecule tmp = null;
// Obtención de objeto molécula
try {
tmp = (Molecule)sp.parseSmiles(smiles);
} catch (InvalidSmilesException e) {
// TODO Auto-generated catch block
System.out.println(" ERROR pasando smiles a
molecula: "+e);
}
// Generación de coordenadas
StructureDiagramGenerator sdg = new
StructureDiagramGenerator();
sdg.setMolecule(tmp);
try {
sdg.generateCoordinates();
} catch (Exception e) {
// TODO Auto-generated catch block
System.out.println(" ERROR obteniendo coordenadas
desde smiles: "+e);
}
m = (Molecule)sdg.getMolecule();
MoleculeViewer2D mv = new MoleculeViewer2D(m);
mv.display(m, false, true, 2, " MCS para el smiles
"+smiles);
return m;
}
Thank you!!
-----Mensaje original-----
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En nombre de
Rajarshi Guha
Enviado el: miércoles, 21 de noviembre de 2007 21:43
Para: Javi Muriel Zafra
CC: cdk-user@lists.sourceforge.net
Asunto: Re: [Cdk-user] Store molecules in a database
On Nov 21, 2007 3:32 PM, Javi Muriel Zafra <[EMAIL PROTECTED]> wrote:
>
> As I said before, I work with a group of molecules, so a smiles is
> being processed, for example, is this:
>
> CC1C=CC(=CC1)S(=O)ON
>
> Other smiles can be the following:
>
> NOS(=O)C=1C=CCCC=1
> CCCOC(=O)C1C=CC(=CC1)S(=O)ON
The CDK display code displays them nicely.
See
http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws.html#sd
g
--
Rajarshi Guha
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