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")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)## [,1]
## smiles "[C@H]23C1=C(C=C(C=C1OC([C@@H]2CCC(=C3)C)(C)C)CCCCC)O"
## names "(6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol"
## iupac_name "(6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol"
## cas "5957-27-7"
## inchi "InChI=1/C21H30O2/c1-5-6-7-8-15-12-18(22)20-16-11-14(2)9-10-17(16)21(3,4)23-19(20)13-15/h11-13,16-17,22H,5-10H2,1-4H3/t16-,17-/m1/s1"
## stdinchi "InChI=1S/C21H30O2/c1-5-6-7-8-15-12-18(22)20-16-11-14(2)9-10-17(16)21(3,4)23-19(20)13-15/h11-13,16-17,22H,5-10H2,1-4H3/t16-,17-/m1/s1"
## inchikey "InChIKey=CYQFCXCEBYINGO-IAGOWNOFNA-N"
## stdinchikey "InChIKey=CYQFCXCEBYINGO-IAGOWNOFSA-N"
## ficts "D6DB420FE104B075-FICTS-01-3A"
## ficus "D6DB420FE104B075-FICuS-01-5B"
## uuuuu "03D2FB2779F109C1-uuuuu-01-04"
## image "http://cactus.nci.nih.gov/chemical/structure/CYQFCXCEBYINGO-IAGOWNOFSA-N/image"
## file "C21H30O2"
## mw "314.4668"
## monoisotopic_mass "314.2246"
## chemspider_id "15266"
## pubchem_sid "24701569"
## chemnavigator_sid "28846069"
## formula "C21H30O2"
## chemnavigator_sid "28846069"
Show structures.
library(caTools)
image.url <- as.character(translations$image[1])
gif <- read.gif(image.url, verbose = TRUE, flip = TRUE)## GIF image header
## Global colormap with 32 colors
## Comment Extension
## Image [250 x 250]: 1114 bytes
par(pin = c(3.5, 3.5))
image(gif$image, col = gif$col, main = as.character(translations$name[1]), frame.plot = FALSE,
xaxt = "n", yaxt = "n")