Hi, There is a way to get different graphs for the same molecule, but there will be quite a few of them for camphor. It has 11 atoms, and only one permutation that is automorphic (swapping the methyl groups attached to the bridgehead carbon), so there are 11! / 2 = 19,958,400 permutations of the atoms. I'm not sure if there is a way to cut down this number.
gilleain torrance On Mon, Mar 22, 2010 at 8:41 PM, JEAN MARC NUZILLARD <jm.nuzill...@univ-reims.fr> wrote: > Hi, > > 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. > The molecule is camphor. I am usign CDK-1.2.5. > > Is there a non-deterministic part in the SDG algorithm? > Is there a way to purposely get different graphs for the same molecule, > thus allowing the user to choose the best looking one? > > Jean-Marc Nuzillard > www.univ-reims.fr/LSD > > > > ------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------ 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
