In dgrapov/CIRgetR: R interface for chemical identifier translation through the Chemical Identifier Resolver (CIR)

CIRgetR

R interface for chemical identifier translation through the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.

Install package.

install.packages("devtools");install.packages("RJSONIO")
library(devtools);library(RJSONIO)

install_github(repo = "CIRgetR", username = "dgrapov")
library(CIRgetR)

#to show gif
install.packages("caTools")

install.packages("devtools");install.packages("RJSONIO")
library(devtools);library(RJSONIO)

install_github(repo = "CIRgetR", username = "dgrapov")
library(CIRgetR)

Try translating inchi codes.

#test
id<-"CYQFCXCEBYINGO-IAGOWNOFSA-N"
opts<-c("smiles", "names", "iupac_name", "cas", "inchi", "stdinchi", "inchikey", "stdinchikey",
        "ficts", "ficus", "uuuuu", "image", "file", "mw", "monoisotopic_mass","chemspider_id",
        "pubchem_sid", "chemnavigator_sid", "formula", "chemnavigator_sid")     

translations<-lapply(1:length(opts), function(i)
    {
        CIRgetR(id=id,to=opts[i],return.all=FALSE, progress=FALSE)
    })
translations<-do.call("cbind",translations)
t(translations)

Show structures.

library(caTools)
image.url<-as.character(translations$image[1])
gif <- read.gif(image.url, verbose = TRUE, flip = TRUE)
par(pin=c(3.5,3.5))
image(gif$image, col = gif$col, main =as.character(translations$name[1]), frame.plot=FALSE,xaxt="n", yaxt="n") 

dgrapov/CIRgetR documentation built on May 15, 2019, 7:21 a.m.