diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 39 |
1 files changed, 18 insertions, 21 deletions
@@ -28,6 +28,7 @@ #' @importFrom webchem get_cid cid_compinfo #' @importFrom grImport PostScriptTrace readPicture #' @importFrom yaml yaml.load_file +#' @importFrom rsvg rsvg_ps #' @field identifier The identifier that was used to initiate the object, with attribute 'source' #' @field inchikey InChI Key, with attribute 'source' #' @field smiles SMILES code, with attribute 'source' @@ -193,26 +194,22 @@ chent <- R6Class("chent", PythonInR::pyExec("d2d.DrawMolecule(mol)") PythonInR::pyExec("d2d.FinishDrawing()") self$svg <- PythonInR::pyGet("d2d.GetDrawingText()") - - if (!requireNamespace("grConvert")) { - stop("grConvert is not available, self$Picture will not be created") - } else { - # Convert to PostScript, remembering size properties - svgfile <- tempfile(fileext = ".svg") - writeLines(self$svg, svgfile) - psfile <- tempfile(fileext = ".ps") - suppressMessages(grConvert::convertPicture(svgfile, psfile)) - ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1] - ps_font_size <- gsub(" .*$", "", ps_font_line) - self$Pict_font_size = as.numeric(ps_font_size) - - # Read in to create Picture - xmlfile <- tempfile(fileext = ".xml") - PostScriptTrace(psfile, outfilename = xmlfile) - unlink(paste0("capture", basename(psfile))) - self$Picture <- readPicture(xmlfile) - unlink(c(xmlfile, psfile, svgfile)) - } + svgfile <- tempfile(fileext = ".svg") + psfile <- tempfile(fileext = ".ps") + writeLines(self$svg, svgfile) + rsvg::rsvg_ps(svgfile, psfile) + + # Get size properties useful for plotting + ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1] + ps_font_size <- gsub(" .*$", "", ps_font_line) + self$Pict_font_size = as.numeric(ps_font_size) + + # Read in to create Picture + xmlfile <- tempfile(fileext = ".xml") + PostScriptTrace(psfile, outfilename = xmlfile) + unlink(paste0("capture", basename(psfile))) + self$Picture <- readPicture(xmlfile) + unlink(c(xmlfile, psfile, svgfile)) }, get_chyaml = function(repo = c("wd", "local", "web"), chyaml = paste0(URLencode(self$identifier), ".yaml")) { @@ -610,7 +607,7 @@ rdkit_available <- function() PythonInR::pyConnect() } sink(tempfile()) - try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"), + try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"), silent = TRUE) sink() if (inherits(try_rdkit, "try-error")) { |