diff options
Diffstat (limited to 'R/chent.R')
| -rw-r--r-- | R/chent.R | 62 |
1 files changed, 30 insertions, 32 deletions
@@ -5,7 +5,7 @@ #' generated using RDKit if RDKit and its python bindings are installed. #' #' @export -#' @format An \code{\link{R6Class}} generator object +#' @format An [R6Class] generator object #' @importFrom R6 R6Class #' @importFrom utils URLencode #' @importFrom webchem get_cid cid_compinfo @@ -79,7 +79,7 @@ chent <- R6Class("chent", #' @field svg SVG code svg = NULL, - #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport + #' @field Picture Graph as a [grImport::Picture-class] object obtained using the grImport package Picture = NULL, #' @field Pict_font_size Font size as extracted from the intermediate PostScript file @@ -123,22 +123,8 @@ chent <- R6Class("chent", } if (rdkit) { - if(rdkit_available) { - if (is.null(self$smiles)) { - message("RDKit would need a SMILES code") - } else { - available_smiles <- names(self$smiles) - smiles_preference <- c("user", "PubChem_Isomeric", "PubChem_Canonical") - smiles_preferred_i <- min(match(available_smiles, smiles_preference)) - smiles_preferred <- smiles_preference[smiles_preferred_i] - - message("Trying to get chemical information from RDKit using ", - smiles_preferred, " SMILES\n", - self$smiles[smiles_preferred]) - self$get_rdkit(template = template) - self$mw <- self$rdkit$mw - attr(self$mw, "source") <- "rdkit" - } + if (rdkit_available) { + self$get_rdkit(template = template) } else { message("RDKit is not available") } @@ -154,11 +140,11 @@ chent <- R6Class("chent", attr(self$smiles, "source") <- "user" } if (is.null(self$inchikey)) { - self$inchikey<- NA + self$inchikey <- NA attr(self$inchikey, "source") <- "user" } if (is.null(self$mw)) { - self$mw<- NA + self$mw <- NA attr(self$mw, "source") <- "user" } @@ -187,16 +173,16 @@ chent <- R6Class("chent", get_pubchem = function(pubchem_cid) { self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid", properties = c("MolecularFormula", "MolecularWeight", - "CanonicalSMILES", "IsomericSMILES", + "ConnectivitySMILES", "SMILES", "InChI", "InChIKey", "IUPACName", "XLogP", "TPSA", "Complexity", "Charge", "HBondDonorCount", "HBondAcceptorCount"))) - self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]] + self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from = "cid")[[1]] - self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSMILES + self$smiles["PubChem"] <- self$pubchem$SMILES - if (self$pubchem$IsomericSMILES != self$pubchem$CanonicalSMILES) { - self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSMILES + if (self$pubchem$SMILES != self$pubchem$ConnectivitySMILES) { + self$smiles["PubChem_Connectivity"] <- self$pubchem$ConnectivitySMILES } self$mw = as.numeric(self$pubchem$MolecularWeight) @@ -233,17 +219,29 @@ 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 (!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)) + smiles_preferred <- smiles_preference[smiles_preferred_i] + + message("Trying to get chemical information from RDKit using ", + smiles_preferred, " SMILES\n", + self$smiles[smiles_preferred]) self$rdkit <- list() self$mol <- rdkit_module$Chem$MolFromSmiles(self$smiles[1]) self$rdkit$mw <- rdkit_module$Chem$Descriptors$MolWt(self$mol) - if (!is.null(self$mw)) { + if (!is.na(self$mw)) { if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { message("RDKit mw is ", self$rdkit$mw) message("mw is ", self$mw) } + } else { + self$mw <- self$rdkit$mw + attr(self$mw, "source") <- "rdkit" } # Create an SVG representation @@ -630,7 +628,7 @@ draw_svg.chent = function(x, width = 300, height = 150, #' #' @importFrom grImport grid.picture #' @param x The chent object to be plotted -#' @param ... Further arguments passed to \code{\link{grid.picture}} +#' @param ... Further arguments passed to [grImport::grid.picture] #' @export #' @examples #' caffeine <- chent$new("caffeine") @@ -652,7 +650,7 @@ plot.chent = function(x, ...) { #' [bcpc_query][webchem::bcpc_query]. #' #' @export -#' @format An \code{\link{R6Class}} generator object +#' @format An [R6::R6Class] generator object #' @examples #' # On Travis, we get a certificate validation error, #' # likely because the system (xenial) is so old, @@ -776,7 +774,7 @@ print.pai = function(x, ...) { #' product #' #' @export -#' @format An \code{\link{R6Class}} generator object. +#' @format An [R6::R6Class] generator object. ppp <- R6Class("ppp", public = list( |