LSP Cheminformatics R client

The R client provides easy access to the functionality provided by the LSP Cheminformatics server.

Installing the R client

devtools::install_github("labsyspharm/lsp-cheminformatics", subdir = "lsp_cheminf_rclient")

The client only functions while the lspcheminf server is running.

Query for similarities

The R client can be used to query the chemical similarity between compounds. By default the Morgan fingerprinting algorithm is used.

library(lspcheminf)
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

If we want to compute the similarity based on topological fingerprints instead and pass some custom arguments to the RDKit function we can do this:

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)"
),
fingerprint_type = "topological",
fingerprint_args = list("minPath" =  2, "useHs" = FALSE)
)
#> # A tibble: 2 x 3
#>   query        score target
#>   <chr>        <dbl> <chr>
#> 1 resveratrol 0.0967 tofacitnib
#> 2 resveratrol 0.198  aspirin

Query for substructure matches

match_substructure(
  c("secondary_amine" = "[H]N(C)C"),
  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)"
  ),
  query_identifier = "smiles"
)
#> # A tibble: 1 x 3
#>   match      query           target
#>   <list>     <chr>           <chr>
#> 1 <list [6]> secondary_amine tofacitnib

Six matches for secondary amine groups where found in tofacitnib. The atom indices for each match are stored in the match list column.

Additional functionality

All additional functionality is documented in the Reference