In NIVANorge/chemspiderapi: R Wrapper for ChemSpider's API Services

MOL files are returned by multiple possible API queries. Most obviously by get_recordId_mol(), but also as part of get_recordId_details(). Saving those human-readable MOL files from R is possible with base R functionality.

Downloading the MOL file of caffeine

For demonstration purposes, we will work with the MOL file for caffeine. Before starting, we need to load the chemspiderapi package and retrieve the API key. See the separate vignette "Storing and Accessing API Keys" for details on handling API keys using the keyring package.

library(chemspiderapi)

apikey <- keyring::key_get(service = "ChemSpider API key", username = Sys.getenv("USERNAME"))

We can now get the MOL file for caffeine, which has a ChemSpider ID of 2424.

caffeine_mol <- get_recordId_mol(recordId = 2424L, apikey = apikey)

caffeine_mol

length(caffeine_mol)

Sys.sleep(5)

Saving the MOL file

Saving the file is done using the writeLines() function. Note that the file is specified as a connection.

con <- file("caffeine.mol")

writeLines(caffeine_mol, con = con)

close(con)

Saving SDF files

Similar to the above procedure, bulk files SDF files containing multiple MOL entries can be stored. SDF files would be the result of queries by, for example, post_mass(). Accordingly, only the file connection needs to be changed. The below example is looking at chemicals with a mass and range similar to caffeine. First the queryId is obtained.

queryId <- post_mass(mass = 194, range = 0.002, apikey = apikey)

Next, the status is controlled.

status <- get_queryId_status(queryId = queryId, count = FALSE, message = FALSE, apikey = apikey)

status

The SDF file can now be retrieved. Note that per default, the SDF file is decompressed.

caffeine_sdf <- get_queryId_results_sdf(queryId = queryId, status = status, apikey = apikey)

head(caffeine_sdf)

length(caffeine_sdf)

The file can now be written.

con <- file("caffeine.sdf")

writeLines(caffeine_sdf, con = con)

close(con)

NIVANorge/chemspiderapi documentation built on Jan. 10, 2021, 10:12 a.m.