dimethylether = cdk.fromSMILES( "COC" );You can see four of my favorite cheminformatics tools integrated: CDK is used to convert a SMILES into connection table with add explicit hydrogens, and to create initial 3D coordinates (with the code from Christian Hoppe, and thanx to Stefan for fixing that code in the CDK 1.1.x branch!). Then, CMLDOM is used to create and save a CML document, which is then opened into a Jmol editor in Bioclipse.
cdk.addExplicitHydrogens( dimethylether );
cdk.generate3dCoordinates( dimethylether );
// save as CML
cdk.saveCML( dimethylether, "/Virtual/dimethylether.cml" );
ui.open( "/Virtual/dimethylether.cml" ); // this should open a JmolEditor
jmol.minimize();
A variation of this script is visible in the following screenshot:
