Calculate chemical similarity between compounds.

Calculate chemical similarity between compounds.

chemical_similarity(
  query,
  target = NULL,
  fingerprint_type = c("morgan", "topological"),
  fingerprint_args = NULL,
  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.
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(
  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)"
  )
)
#> # A tibble: 2 x 3
#>   query        score target    
#>   <chr>        <dbl> <chr>     
#> 1 resveratrol 0.0571 tofacitnib
#> 2 resveratrol 0.132  aspirin