diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 106 |
1 files changed, 85 insertions, 21 deletions
@@ -17,21 +17,27 @@ #' An R6 class for chemical entities with associated data #' -#' The class is initialised with an identifier. Chemical information is retrieved -#' from the internet. +#' 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. #' #' @docType class #' @export #' @format An \code{\link{R6Class}} generator object #' @importFrom R6 R6Class #' @importFrom webchem get_cid cid_compinfo +#' @importFrom grImport PostScriptTrace readPicture +#' @importFrom PythonInR pyIsConnected pyConnect pyImport pyExec pyExecg +#' @importFrom yaml yaml.load_file #' @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' #' @field mw Molecular weight, with attribute 'source' #' @field pubchem List of information retreived from PubChem #' @field rdkit List of information obtained with RDKit -#' @example inst/examples/chents.R +#' @field Picture Graph as a \code{\link{picture}} object obtained using grImport +#' @example inst/examples/octanol.R +#' @example inst/examples/caffeine.R #' @keywords data chent <- R6Class("chent", @@ -42,6 +48,8 @@ chent <- R6Class("chent", mw = NULL, pubchem = NULL, rdkit = NULL, + Picture = NULL, + chyaml = NULL, initialize = function(identifier, smiles = NULL, source = c("rdkit", "pubchem")) { self$identifier <- identifier @@ -96,25 +104,41 @@ chent <- R6Class("chent", } }, get_rdkit = function() { - if (require(PythonInR)) { - id <- names(self$identifier) - try_rdkit <- try(pyImport("Chem", from = "rdkit")) - if (inherits(try_rdkit, "try-error")) { - message("Could not import RDKit in Python session") - } else { - self$rdkit <- list() - pyImport("Descriptors", from = "rdkit.Chem") - pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles, "')")) - self$rdkit$mw <- pyExecg("mw = Descriptors.MolWt(mol)", "mw") - if (!is.null(self$mw)) { - if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { - message("RDKit mw is ", self$rdkit$mw) - message("mw is ", self$mw) - } + id <- names(self$identifier) + if (!pyIsConnected()) { + pyConnect() + } + try_rdkit <- try(pyImport("Chem", from = "rdkit")) + if (inherits(try_rdkit, "try-error")) { + message("Could not import RDKit in Python session") + } else { + self$rdkit <- list() + pyImport("Descriptors", from = "rdkit.Chem") + pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles, "')")) + self$rdkit$mw <- pyExecg("mw = Descriptors.MolWt(mol)", "mw") + if (!is.null(self$mw)) { + if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { + message("RDKit mw is ", self$rdkit$mw) + message("mw is ", self$mw) } } - } else { - stop("rdkit not available as PythonInR is not installed") + + # Create a grImport Picture + pyImport("Draw", from = "rdkit.Chem") + psfile <- tempfile(fileext = ".ps") + xmlfile <- tempfile(fileext = ".xml") + cmd <- paste0("Draw.MolToFile(mol, '", psfile, "')") + pyExec(cmd) + PostScriptTrace(psfile, outfilename = xmlfile) + unlink(paste0("capture", basename(psfile))) + self$Picture <- readPicture(xmlfile) + } + }, + get_chyaml = function(repo = c("local", "web")) { + repo = match.arg(repo) + if (repo == "local") { + self$chyaml = yaml.load_file(file.path("~", "git/chyaml", + paste0(URLencode(self$identifier), ".yaml"))) } }, TPs = list(), @@ -158,6 +182,7 @@ chent <- R6Class("chent", stringsAsFactors = FALSE), add_soil_degradation_endpoints = function(destination, DT50 = NA, comment = "", pages = NA) { + if (length(pages) > 1) pages = paste(pages, collapse = ", ") i <- nrow(self$soil_degradation_endpoints) + 1 self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- c(destination, comment, pages) @@ -183,6 +208,45 @@ print.chent = function(x, ...) { } } +#' Draw SVG graph from a chent object using RDKit +#' +#' @importFrom PythonInR pyIsConnected pyConnect pyImport pyExec +#' @param x The chent object to be plotted +#' @param width The desired width in pixels +#' @param height The desired height in pixels +#' @param filename The filename +#' @param subdir The path to which the file should be written +#' @export +draw_svg.chent = function(x, width = 300, height = 150, + filename = paste0(names(x$identifier), ".svg"), + subdir = "svg") { + if (!pyIsConnected()) { + pyConnect() + } + try_rdkit <- try(pyImport("Chem", from = "rdkit")) + if (inherits(try_rdkit, "try-error")) { + message("Could not import RDKit in Python session") + } else { + if (!dir.exists(subdir)) dir.create(subdir) + pyExec(paste0("mol = Chem.MolFromSmiles('", x$smiles, "')")) + pyImport("Draw", from = "rdkit.Chem") + cmd <- paste0("Draw.MolToFile(mol, '", file.path(subdir, filename), + "', size = (", width, ", ", height, "))") + pyExec(cmd) + } +} + +#' Plot method for chent objects +#' +#' @importFrom grImport grid.picture +#' @param x The chent object to be plotted +#' @param ... Further arguments passed to \code{\link{grid.picture}} +#' @example inst/examples/caffeine.R +#' @export +plot.chent = function(x, ...) { + grid.picture(x$Picture) +} + #' An R6 class for pesticidal active ingredients and associated data #' #' The class is initialised with an identifier which is generally an ISO common name. @@ -194,7 +258,7 @@ print.chent = function(x, ...) { #' @format An \code{\link{R6Class}} generator object #' @field iso ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides #' @field alanwood List of information retreived from www.alanwood.net/pesticides -#' @example inst/examples/ai.R +#' @example inst/examples/pai.R #' @keywords data pai <- R6Class("pai", |