[BioC] ChemmineR Help

[Thomas Girke]

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