Find chemical similarity matches up to a threshold.

Requires chemfp installed on the python server.

chemical_similarity_threshold(
  query,
  target = NULL,
  fingerprint_type = c("morgan", "topological"),
  fingerprint_args = NULL,
  threshold = 0.7,
  n_threads = 1,
  url = "http://127.0.0.1:8000"
)

Arguments

query	A character vector of compounds, optionally named. Assumed to be InChI. Specify descriptor explicitly or attach pre-computed fingerprints using compounds(). Pre-computed fingerprints are used instead of chemical descriptors if given. All similarities between the query and the target compounds are calculated.
target	A character vector of compounds like query. If not given, the similarities of all pairwise combinations between query compounds are calculated.
fingerprint_type	Calculate morgan or topological fingerprints.
fingerprint_args	Optional list of additional arguments to the RDKit fingerprinting function.
threshold	A double between 0 and 1 representing the minimum reported similarity.
n_threads	Number of threads used to process the query
url	URL to the lspcheminf python server

Value

A tibble with three columns, containing names of query and target compounds and their similarity.

Examples

chemical_similarity_threshold(
  c("resveratrol" = "InChI=1S/C14H12O3/c15-12-5-3-10(4-6-12)1-2-11-7-13(16)9-14(17)8-11/h1-9,15-17H/b2-1+"),
  c(
    "tofacitnib" = "InChI=1S/C16H20N6O/c1-11-5-8-22(14(23)3-6-17)9-13(11)21(2)16-12-4-7-18-15(12)19-10-20-16/h4,7,10-11,13H,3,5,8-9H2,1-2H3,(H,18,19,20)/t11-,13+/m1/s1",
    "aspirin" = "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"
  ),
  threshold = 0.1
)
#> # A tibble: 1 x 3
#>   query       score target 
#>   <chr>       <dbl> <chr>  
#> 1 resveratrol 0.132 aspirin
chemical_similarity_threshold(
    compounds(
      c("a" = "880DF", "b" = "881DF", "c" = "870E0"),
      descriptor = "fingerprint"
    ),
    threshold = 0.8
)
#> # A tibble: 1 x 3
#>   query score target
#>   <chr> <dbl> <chr> 
#> 1 a     0.929 b