On 25 March 2010 06:54, Sam Adams <se...@cam.ac.uk> wrote: > > If the process involves iterating through a HashMap or HashSet at any > point that could be the cause of the non-determinism. > > Switching to a CCG-like algorithm will make the non-determinism worse. > As I understand it, their layout algorithm is inherently random: the > structure is fragmented into component blocks - rings, chains, groups > etc, and sets of constraints/possible layouts generated for each block. > As the number of blocks increases this rapidly leads to an explosion in > the number of possible combinations of layouts, so a reasonable solution > is found by stochastic sampling.
Set the random seed? > Sam > > > On 25/03/2010 00:35, Christoph Steinbeck wrote: >> 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 >> > > > ------------------------------------------------------------------------------ > 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
