get_csid: ChemSpider ID from compound name, formula, SMILES, InChI or...
In ropensci/webchem: Chemical Information from the Web

get_csid

R Documentation

ChemSpider ID from compound name, formula, SMILES, InChI or InChIKey

Description

Query one or more compunds by name, formula, SMILES, InChI or InChIKey and return a vector of ChemSpider IDs.

Usage

get_csid(
  query,
  from = c("name", "formula", "inchi", "inchikey", "smiles"),
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  apikey = NULL,
  ...
)

Arguments

`query`	character; search term.
`from`	character; the type of the identifier to convert from. Valid values are `"name"`, `"formula"`, `"smiles"`, `"inchi"`, `"inchikey"`. The default value is `"name"`.
`match`	character; How should multiple hits be handled?, "all" all matches are returned, "best" the best matching is returned, "ask" enters an interactive mode and the user is asked for input, "na" returns NA if multiple hits are found.
`verbose`	logical; should a verbose output be printed on the console?
`apikey`	character; your API key. If NULL (default), `cs_check_key()` will look for it in .Renviron or .Rprofile.
`...`	furthrer arguments passed to `cs_control`

Details

Queries by SMILES, InChI or InChiKey do not use cs_control options. Queries by name use order_by and order_direction. Queries by formula also use datasources. See cs_control() for a full list of valid values for these control options.

formula can be expressed with and without LaTeX syntax.

Value

Returns a tibble.

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & conditions: https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v093.i13")}.

Examples

## Not run: 
get_csid("triclosan")
get_csid(c("carbamazepine", "naproxene","oxygen"))
get_csid("C2H6O", from = "formula")
get_csid("C_{2}H_{6}O", from = "formula")
get_csid("CC(O)=O", from = "smiles")
get_csid("InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)", from = "inchi")
get_csid("QTBSBXVTEAMEQO-UHFFFAOYAR", from = "inchikey")

## End(Not run)

ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.