Question: How do I convert kegg info on drug to a format allowing me to calculate similarities?
0
gravatar for Joris.Meys
21 months ago by
Joris.Meys0
Belgium
Joris.Meys0 wrote:

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.

graph chemminer keggrest fmcsr • 391 views
ADD COMMENTlink modified 21 months ago by jennietodd1410 • written 21 months ago by Joris.Meys0
Answer: How do I convert kegg info on drug to a format allowing me to calculate similari
1
gravatar for Thomas Girke
21 months ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:

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

Thomas

ADD COMMENTlink written 21 months ago by Thomas Girke1.7k

Thank you incredibly much, this is wonderful.

ADD REPLYlink written 21 months ago by Joris.Meys0
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