diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 15 |
1 files changed, 12 insertions, 3 deletions
@@ -40,6 +40,8 @@ #' @param file The file to write to #' @param dir The directory to write the file to #' @examples +#' # Don't run examples per default, as PubChem may be unavailable +#' \dontrun{ #' caffeine <- chent$new("caffeine") #' print(caffeine) #' if (!is.null(caffeine$Picture)) { @@ -47,6 +49,7 @@ #' } #' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) #' print(oct) +#' } chent <- R6Class("chent", public = list( #' @field identifier (`character(1)`)\cr @@ -219,10 +222,10 @@ chent <- R6Class("chent", #' @description #' Get chemical information from RDKit if available get_rdkit = function(template = NULL) { - + if (!rdkit_available) stop("RDKit is not available") if (is.null(self$smiles)) stop("RDKit would need a SMILES code") - + available_smiles <- names(self$smiles) smiles_preference <- c("user", "PubChem", "PubChem_Connectivity") smiles_preferred_i <- min(match(available_smiles, smiles_preference)) @@ -492,7 +495,7 @@ chent <- R6Class("chent", #' @param N The Freundlich exponent #' @param perc_clay The percentage of clay in the soil #' @param CEC The cation exchange capacity - add_soil_sorption = function(soils, + add_soil_sorption = function(soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, @@ -630,11 +633,14 @@ draw_svg.chent = function(x, width = 300, height = 150, #' @param ... Further arguments passed to [grImport::grid.picture] #' @export #' @examples +#' # Don't run examples per default, as PubChem may be unavailable +#' \dontrun{ #' caffeine <- chent$new("caffeine") #' print(caffeine) #' if (!is.null(caffeine$Picture)) { #' plot(caffeine) #' } +#' } plot.chent = function(x, ...) { if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?") grid.picture(x$Picture) @@ -651,6 +657,8 @@ plot.chent = function(x, ...) { #' @export #' @format An [R6::R6Class] generator object #' @examples +#' # Don't run examples per default, as PubChem may be unavailable +#' \dontrun{ #' atr <- pai$new("atrazine") #' print(atr) #' if (!is.null(atr$Picture)) { @@ -659,6 +667,7 @@ plot.chent = function(x, ...) { #' # We can also define pais that are not found on the BCPC site #' decanol <- pai$new("1-Decanol") #' print(decanol) +#' } pai <- R6Class("pai", inherit = chent, public = list( |