I downloaded some information from KEGG using KEGGREST:

library(KEGGREST)
query <- keggGet(c("D00040", "D00066"))

Now I want to be able to convert this to the ChemmineR SDF format so I can use the fmcsBatch function from fmcsr. Problem is that I'm not terribly familiar with these formats, and looking at the structure of the sdfsample data didn't really help either...

library(ChemmineR)
data(sdfsample)
str(sdfsample[1])
#> Formal class 'SDFset' [package "ChemmineR"] with 2 slots
#>  ..@ SDF:List of 1
#>  .. ..$ :Error in FUN(X[[i]], ...) : 
#>  no slot of name "version" for this object of class "SDF"

Anyone who can give me some pointers? I'd be happy with extracting eg the pubChem IDs and finding a way to download the sdf files from there. But doing so manually is not really an option.

Many options exist to address this need. Here are just a few using your specific example: https://gist.github.com/tgirke/fb4d7ab4cc555968b521f4d8e624cd79.

Thomas