Hi, this is a known problem with my SDG code. In fact, if you do the layout a couple of times in a row, you might get different results. I assume that this is due to rounding errors. Definitely, there is no intended random element. The algorithm should, in theory, be deterministic. We have advertised a student project to get the layout closer to something like the CCG people published in JCIM some years ago. (http://www.ebi.ac.uk/steinbeck/projects.html)
Cheers, Chris On 22/03/2010 13:41, JEAN MARC NUZILLARD 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 -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 Video meliora proboque deteriora sequor. ... Ovid, Metamorphoses VII, 20/21 ------------------------------------------------------------------------------ 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
