Message de Sam Adams <[email protected]>: > > If the process involves iterating through a HashMap or HashSet at any > point that could be the cause of the non-determinism.
I confirm: From the Java documentation about HashMap: ... This class makes no guarantees as to the order of the map; in particular, it does not guarantee that the order will remain constant over time... The same for HashSet. The Java documentation does not reveal the reason for which the order may vary over time, but we have not to wonder if it does. The interesting side-effect is that the SDG in the CDG can offer different drawings for the price of one! Thank you for all your answers. Jean-Marc www.univ-reims.fr/LSD > > 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. > > 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 >>> [email protected] >>> 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 > [email protected] > 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 [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
