tag:blogger.com,1999:blog-17889588.post8759123683387447563..comments2024-03-13T07:14:55.283+01:00Comments on chem-bla-ics: Profiling the CDK atom typerEgon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-17889588.post-90703677630738377082008-08-16T12:24:00.000+02:002008-08-16T12:24:00.000+02:00Sounds familiar and I am not surprised, JOELib2 us...Sounds familiar and I am not surprised, JOELib2 uses a lot of reflection patterns for flexibility, but the time requirements are not optimal since this is done even on atom and bond level.<BR/><BR/>I guess on the long term the only flexible and speedup workaround would be a compiler-compiler solution instead of reflection. Especially with the goal to create as much caching as possible, minimize expensive object or reflection object creations by pushing such things to a higher level or changing data structures.Anonymoushttps://www.blogger.com/profile/09112376168632883058noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-84157201196884468092008-08-15T07:59:00.000+02:002008-08-15T07:59:00.000+02:00Yeah, should have copied those numbers in the scre...Yeah, should have copied those numbers in the screenshot too... Sorry about that.<BR/><BR/>174 nitrogens (~77% of the time), 528 carbons (~13% of the time), etc...<BR/><BR/>It's really out of proportion. The screenshot does show that ring detection is the problem, which is a required step, but it really worries me that the loadClassInternal() explains so much of this time...<BR/><BR/>I've spoken with the people from Classpath, and they recommended longer profiling runs; this was just 15 seconds (1.5 seconds of not profiling); and it might simply be JVM start up issues (though the RingSet loading is long after all other IChemObject classes are loaded). I'll rerun the profiling against the 1000 ZINC structures asap.Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-86785535932169015122008-08-14T23:30:00.000+02:002008-08-14T23:30:00.000+02:00Might it be the case that there are more N atom ty...Might it be the case that there are more N atom types than other atom types?Rajarshihttps://www.blogger.com/profile/17004737222701996223noreply@blogger.com