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Retrieve chemical structure data for GSRS substances

Source: R/gsrs_structure.R
gsrs_structure.Rd

For each supplied UNII, fetches the full substance record from GET /api/v1/substances(<UNII>) and extracts the embedded structure object, returning chemical identifiers and properties as a tidy data frame.

Usage

gsrs_structure(unii, verbose = TRUE, delay = 0.5)

Arguments

unii

Character vector of one or more UNII codes.

verbose

Logical. If TRUE, emit progress messages. Default TRUE.

delay

Numeric. Seconds to wait between individual lookups when unii has multiple entries. Default 0.5.

Value

A data frame with columns:

smiles

Canonical SMILES string.

formula

Molecular formula (e.g., "C9H8O4").

mwt

Molecular weight (numeric).

inchi_key

Standard InChIKey.

inchi

Full InChI string.

stereochemistry

Stereochemistry descriptor (e.g., "ACHIRAL", "RACEMIC", "ABSOLUTE").

optical_activity

Optical activity (e.g., "UNSPECIFIED", "(+)", "(-)").

charge

Formal charge (integer).

stereo_centers

Number of stereocenters.

defined_stereo

Number of defined stereocenters.

ez_centers

Number of E/Z double-bond stereocenters.

molfile

MDL molfile as a string.

date_retrieved

Date the response was received.

query

The UNII supplied by the caller.

Non-chemical substances (proteins, polymers, etc.) return a row of NAs with query set. Returns NULL on error (with a warning).

See also

gsrs_substance(), gsrs_structure_search(), gsrs_names(), gsrs_codes()

Examples

# \donttest{
  Sys.sleep(2)
  out <- gsrs_structure("R16CO5Y76E")  # aspirin
#> ℹ Fetching structure for UNII: R16CO5Y76E ...
#> ℹ Retrieved structure for 1 substance(s).
  if (!is.null(out)) print(out[, c("smiles", "formula", "mwt", "inchi_key")])
#>                  smiles formula      mwt                   inchi_key
#> 1 CC(=O)Oc1ccccc1C(=O)O  C9H8O4 180.1578 BSYNRYMUTXBXSQ-UHFFFAOYSA-N
# }