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Search GSRS by chemical structure

Source: R/gsrs_structure_search.R
gsrs_structure_search.Rd

Searches the FDA Global Substance Registration System for substances matching a chemical structure query supplied as a SMILES string. Supports substructure, similarity, exact-match, and flexible (disconnected moiety) search types.

Usage

gsrs_structure_search(
  smiles,
  type = c("sub", "sim", "exact", "flex"),
  cutoff = 0.8,
  top = 10L,
  verbose = TRUE
)

Arguments

smiles

Character string. A valid SMILES or SMARTS string describing the query structure (e.g., "CC(=O)Oc1ccccc1C(=O)O" for aspirin).

type

Character string. Search type. One of:

"sub"

Substructure search (default). Returns all substances whose structure contains the query as a substructure.

"sim"

Similarity search. Returns substances with Tanimoto similarity >= cutoff. Use cutoff to control threshold.

"exact"

Exact structure match (tautomer-aware, stereo-sensitive).

"flex"

Flexible (disconnected moiety) search; stereo-insensitive.

cutoff

Numeric in [0, 1]. Tanimoto similarity cutoff for type = "sim". Default 0.8. Ignored for other search types.

top

Integer. Maximum number of records to return. Default 10.

verbose

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

Value

A data frame with the same columns as gsrs_search(), plus a query_smiles column recording the input SMILES. Returns NULL on error (with a warning).

See also

gsrs_structure(), gsrs_search()

Examples

# \donttest{
  Sys.sleep(2)
  # Exact match for aspirin
  out <- gsrs_structure_search("CC(=O)Oc1ccccc1C(=O)O", type = "exact")
#> ℹ Running exact structure search for: CC(=O)Oc1ccccc1C(=O)O ...
#> ℹ Retrieved 1 matching substance(s).
  if (!is.null(out)) print(out[, c("approval_id", "preferred_name")])
#>   approval_id preferred_name
#> 1  R16CO5Y76E        Aspirin

  Sys.sleep(2)
  # Similarity search
  out_sim <- gsrs_structure_search("CC(=O)Oc1ccccc1C(=O)O",
                                   type = "sim", cutoff = 0.7, top = 5)
#> ℹ Running sim structure search for: CC(=O)Oc1ccccc1C(=O)O ...
#> ℹ Retrieved 5 matching substance(s).
  if (!is.null(out_sim)) print(out_sim[, c("approval_id", "preferred_name")])
#>   approval_id    preferred_name
#> 1  R16CO5Y76E           Aspirin
#> 2  6QT214X4XU         ALOXIPRIN
#> 3  8649Y4P3PA      Zinc Aspirin
#> 4  5XE48797BQ ASPIRIN POTASSIUM
#> 5  E62HT5S2E9    Aspirin sodium
# }