Hi Egon, Message de Egon Willighagen <egon.willigha...@gmail.com>:
> Hi Jean Marc, > > On Mon, Mar 22, 2010 at 9:41 PM, JEAN MARC NUZILLARD > <jm.nuzill...@univ-reims.fr> wrote: >> I created two identical molecules by calling addAtoms and addBonds >> in the same order with the same arguments and then I generated coordinates >> using a StructureDiagramGenerator. >> Looking with Jmol at the molecules in the corresponding SD file, >> it appeared that the graphs were different. >> Repeting the whole process, I sometimes get the same graphs, >> but sometimes different ones. > > I guess, the chemical graphs were identical but the graphics different? Yes. >> The molecule is camphor. I am usign CDK-1.2.5. > Can you perhaps share your code? www.univ-reims.fr/LSD/private/Sol-CDK.tar.gz >> Is there a non-deterministic part in the SDG algorithm? > > Yes, I think there is. > >> Is there a way to purposely get different graphs for the same molecule, >> thus allowing the user to choose the best looking one? > > I am not aware of that option, other than just repeating it. The > suggestion by Gilleain of permuting the atom order might help here > increase the change of a different diagram. No need to change the order of atom numbers. Just rerun the SDG! > > I can also suggest to have a look at the template functionality... > perhaps for your applications there are common structures that you > always want to get the same coordinates. In that case, you could add > templates for those common substructures. Thank you. Jean-Marc www.univ-reims.fr/LSD > > Egon > > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
