Dear Danishuddin, As far as I can tell, the error points to a typo you have in your R code: it cannot find "sdfap" since the correct function name for computing atom pair descriptors is "sdf2ap". Also, if you have only 5000 molecules in your SD file then it may not be necessary to use the sdfStream function which is for processing very large numbers of molecules while minimizing the memory footprint. Importing your SD file directly into an SDFset object with "read.SDFset" will be sufficient. A simple clustering routine with atom pairs/fingerprints and the binning clustering algorithm would look like this: ## Import your own file library(ChemmineR) sdfset <- read.SDFset("your_SD_file") ## Or use sample set provided by ChemmineR for testing data(sdfsample); sdfset <- sdfsample ## Compute atom pairs apset <- sdf2ap(sdfset) # Will run for some minutes ## Or compute atom pair fingerprints fpset <- desc2fp(apset) ## Binning clustering clusters <- cmp.cluster(apset, cutoff = c(0.7, 0.8, 0.9)) ## The result should look similar to this clusters[1:4,] ids CLSZ_0.7 CLID_0.7 CLSZ_0.8 CLID_0.8 CLSZ_0.9 CLID_0.9 48 CMP48 2 48 2 48 2 48 49 CMP49 2 48 2 48 2 48 54 CMP54 2 54 2 54 2 54 55 CMP55 2 54 2 54 2 54 Please also make sure you are running a recent version of R and ChemmineR. The current version of ChemmineR is 2.11.8, which you can check by running the command sessionInfo() in your R session. Thomas On Thu, Nov 29, 2012 at 05:46:02AM +0000, danishuddin --- wrote: > Dear ChemmieR author > > I am a researcher working on chemoinformatics, recently i come to known about the ChemmineR package, > i found it very helpful for my study, firstly i would give you thanks form my side and also from the > side of resercher working on the chemoinforamtic field. Really, this is very helpful. Well, i am new > to this, thus i am facing some problems. I am using the file of 5000 compounds which are in sdf format > for clustering. while using this i got the error. The image of this error i have attach with this mail. > I request you to help me in coming up with this error. I will wait for you response. Please help me. > > > Thanking you > > > Regards > Danishuddin