No. Only 1.5 - actually the main reason the SMILES rewrite. 1.4 will write stereo if given a molecule with 2D coordinates and wedges but since you can’t generate a depiction from SMILES with this (in 1.5) it’s not possible. The stereo written from the 2D depiction also isn’t always corrected.
Cheers, John On Dec 4, 2014, at 6:12 PM, Martin Gütlein <[email protected]> wrote: > Hi, > > is there a way to keep the annotations for stereoisomerism when printing > SMILES with CDK1.4? > Example is below. > > Thanks, > Martin > > String smiles = "C[C@@]1(F)[C@H](O)[C@H](O[C@H]1n1ccc(=O)[nH]c1=O)C=O"; > IAtomContainer compound = new > SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles); > SmilesGenerator smilesGenerator = new SmilesGenerator(); > smilesGenerator.setUseAromaticityFlag(true); > System.out.println(smilesGenerator.createSMILES(compound)); > > StructureDiagramGenerator sdg = new StructureDiagramGenerator(); > sdg.setMolecule((IMolecule) compound); > sdg.generateCoordinates(); > compound = sdg.getMolecule(); > boolean b[] = new boolean[compound.getBondCount()]; > for (int i = 0; i < b.length; i++) > b[i] = true; > System.out.println(smilesGenerator.createChiralSMILES(compound, b)); > > > Output is: > [H]C2(OC([H])(N1CCC(=O)NC1(=O))C(F)(C)C2([H])(O))(C=O) > [H]C2(OC([H])(N1CCC(=O)NC1(=O))C(F)(C)C2([H])(O))(C=O) > > > > > -- > Dipl-Inf. Martin Gütlein > Phone: > +49 (0)6131 39 23336 (office) > +49 (0)177 623 9499 (mobile) > Email: > [email protected] > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
