diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 41 |
1 files changed, 36 insertions, 5 deletions
@@ -36,6 +36,8 @@ #' @field rdkit List of information obtained with RDKit, if installed and #' configured for use with PythonInR #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport +#' @field Pict_font_size Font size as extracted from the intermediate PostScript file +#' @field pdf_height Height of the MediaBox in the pdf after cropping #' @field chyaml List of information obtained from a YAML file #' @field degradation List of degradation endpoints #' @example inst/examples/octanol.R @@ -51,6 +53,8 @@ chent <- R6Class("chent", pubchem = NULL, rdkit = NULL, Picture = NULL, + Pict_font_size = NULL, + pdf_height = NULL, chyaml = NULL, degradation = NULL, initialize = function(identifier, smiles = NULL, smiles_source = 'user', @@ -110,7 +114,12 @@ chent <- R6Class("chent", } }, get_pubchem = function(pubchem_cid) { - self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid")) + self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid", + properties = c("MolecularFormula", "MolecularWeight", + "CanonicalSMILES", "IsomericSMILES", + "InChI", "InChIKey", "IUPACName", + "XLogP", "TPSA", "Complexity", "Charge", + "HBondDonorCount", "HBondAcceptorCount"))) self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]] self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSMILES @@ -171,6 +180,10 @@ chent <- R6Class("chent", xmlfile <- tempfile(fileext = ".xml") cmd <- paste0("Draw.MolToFile(mol, '", psfile, "')") PythonInR::pyExec(cmd) + ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1] + ps_font_size <- gsub(" .*$", "", ps_font_line) + + self$Pict_font_size = as.numeric(ps_font_size) PostScriptTrace(psfile, outfilename = xmlfile) unlink(paste0("capture", basename(psfile))) self$Picture <- readPicture(xmlfile) @@ -263,11 +276,11 @@ chent <- R6Class("chent", if (!exists(to, self$TPs)) stop(to, " was not found in TPs") self$ff[i, ] <- c(from, to, ff, comment, pages) }, - pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures") { - if (!dir.exists("structures")) { + pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf") { + if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") - message("Creating directory '", dir, "'") - dir.create(dir) + message("Trying to create directory '", dir, "'") + dir.create(dir, recursive = TRUE) } path = file.path(dir, file) message("Creating file '", path, "'") @@ -276,6 +289,24 @@ chent <- R6Class("chent", dev.off() message("Cropping file '", path, "' using pdfcrop") system(paste("pdfcrop --margin 10", path, path, "> /dev/null")) + + # Get the height of the MediaBox + head <- readLines(path, n = 20, skipNul = TRUE) + m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE)) + self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) + }, + png = function(file = paste0(self$identifier, ".png"), dir = "structures/png", + antialias = 'gray') { + if (!dir.exists(dir)) { + message("Directory '", dir, "' does not exist") + message("Trying to create directory '", dir, "'") + dir.create(dir, recursive = TRUE) + } + path = file.path(dir, file) + message("Creating file '", path, "'") + png(path, antialias = antialias) + plot(self) + dev.off() } ) ) |