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context("Generation of chent objects")
# Check if we can use RDKit
skip_if_no_rdkit <- function() {
if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
}
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
test_that("We can initialise an object only with identifier and SMILES code", {
expect_equal(oct$identifier, c(X1.octanol = "1-octanol")) # The name of the identifier is generated using make.names()
expect_equal(oct$inchikey, structure(NA, source = "user"))
expect_equal(oct$smiles, c(user = "CCCCCCCCO"))
})
test_that("We can generate a chent object from SMILES using RDKit", {
skip_if_no_rdkit()
oct$get_rdkit()
expect_equivalent(round(oct$mw, 2), 130.23)
})
test_that("We can add information retrieved from PubChem via webchem", {
expect_warning(oct$try_pubchem(), "Overwriting uninitialized InChIKey")
expect_equivalent(round(oct$mw, 2), 130.23)
ik = "KBPLFHHGFOOTCA-UHFFFAOYSA-N"
attr(ik, "source") <- "pubchem"
expect_equal(oct$inchikey, ik)
expect_equal(oct$smiles[["PubChem"]], "CCCCCCCCO")
})
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