Message de Noel O'Boyle <baoille...@gmail.com>: > 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?
Thank you Noel for this question. Non-determinism is not a curse of Heaven (Cosmic rays influence on computers excepted). If some container object uses a random number generator in order to enumerate its content, there should be a way to reset its seed to a given value. Jean-Marc www.univ-reims.fr/LSD > >> 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 > > ------------------------------------------------------------------------------ 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
