Question: fingerprint calculation; chemoinformatics; Problem in rcdk R package
0
gravatar for khanirfanbioinformatics
3.6 years ago by

Hi. I am using smile codes for the FDA approved drugs available in chEMBL 22 database. I am using the r package rcdk and I am using this code

library(rcdk)
dat1<-read.csv("chembl_22_drug_export.txt",sep="\t",header=T)
smi <-lapply(as.character(dat1$CANONICAL_SMILES),parse.smiles)
cmp.fp<-vector("list",nrow(dat1))
## generate fingerprints
for (i in 1:nrow(dat1)){
  cmp.fp[i]<-lapply(smi[[i]][1],get.fingerprint,type="maccs")

}
##Convert fingerprints to matrix form
fpmac<-fp.to.matrix(cmp.fp)
cmp.finger<-as.data.frame(fpmac)

But when I do this step

smi <- lapply(as.character(chembl_22_drug_export$CANONICAL_SMILES), parse.smiles)

I get the following error

Error in .jnew("org/openscience/cdk/smiles/SmilesParser", dcob) : 
  Java Exception <no description because toString() failed>.jnew("org/openscience/cdk/smiles/SmilesParser", dcob)<S4 object of class "jobjRef">

Kindly guide me how do I resolve this error?

R • 1.9k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by khanirfanbioinformatics0

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ADD REPLYlink written 3.6 years ago by WouterDeCoster44k
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