An R6 class for chemical entities with associated data

The class is initialised with an identifier. Chemical information is retrieved from the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed.

Format

An R6Class generator object

Public fields

identifier: (character(1))
The identifier that was used to initiate the object, with attribute 'source'

Methods

Public methods

@@ -767,69 +766,48 @@ Write an EMF image of the structure using -

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
 #> Trying to get chemical information from RDKit using user SMILES
 #> CCCCCCCCO
-#> Did not find chyaml file ./1-octanol.yaml
+#> Error in URLencode(self$identifier): could not find function "URLencode"
 print(oct)
-#> <chent>
-#> Identifier $identifier 1-octanol 
-#> InChI Key $inchikey 
-#> SMILES string $smiles:
-#>        user 
-#> "CCCCCCCCO" 
-#> Molecular weight $mw: 130.2 
+#> Error in eval(expr, envir, enclos): object 'oct' not found
 if (!is.null(oct$Picture)) {
   plot(oct)
 }
+#> Error in eval(expr, envir, enclos): object 'oct' not found
 
 caffeine <- chent$new("caffeine")
 #> PubChem:
 #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
 #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
-#> Did not find chyaml file ./caffeine.yaml
+#> Error in URLencode(self$identifier): could not find function "URLencode"
 print(caffeine)
-#> <chent>
-#> Identifier $identifier caffeine 
-#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>              PubChem_Canonical 
-#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#> Molecular weight $mw: 194.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "caffeine"                "58-08-2"                
-#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
-#>  [5] "Methyltheobromine"       "Theine"                 
-#>  [7] "Thein"                   "Cafeina"                
-#>  [9] "Koffein"                 "Mateina"                
+#> Error in eval(expr, envir, enclos): object 'caffeine' not found
 if (!is.null(caffeine$Picture)) {
   plot(caffeine)
 }
-
+#> Error in eval(expr, envir, enclos): object 'caffeine' not found

- -