diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 103 |
1 files changed, 61 insertions, 42 deletions
@@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2016 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package chents @@ -19,7 +19,7 @@ #' #' 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. +#' python bindings are installed and configured for use with PythonInR. #' #' @docType class #' @export @@ -27,14 +27,14 @@ #' @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 +#' @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 chyaml List of information obtained from a YAML file #' @field degradation List of degradation endpoints @@ -67,15 +67,17 @@ chent <- R6Class("chent", } if (rdkit) { - if (is.null(self$smiles)) { - stop("RDKit needs a SMILES code") - } else { - message("Trying to get chemical information from RDKit using ", - names(self$smiles)[1], " SMILES\n", - self$smiles[1]) - self$get_rdkit() - self$mw <- self$rdkit$mw - attr(self$mw, "source") <- "rdkit" + if(requireNamespace("PythonInR")) { + if (is.null(self$smiles)) { + stop("RDKit needs a SMILES code") + } else { + message("Trying to get chemical information from RDKit using ", + names(self$smiles)[1], " SMILES\n", + self$smiles[1]) + self$get_rdkit() + self$mw <- self$rdkit$mw + attr(self$mw, "source") <- "rdkit" + } } } @@ -89,19 +91,21 @@ chent <- R6Class("chent", if (missing(identifier)) identifier <- self$identifier pubchem_cids = webchem::get_cid(identifier) - if (is.na(pubchem_cids[1])) { - stop("Query ", identifier, " did not give results at PubChem") - } else { - message("Found ", length(pubchem_cids), " entries in PubChem, using the first one.") - self$get_pubchem(pubchem_cids[1]) - } + if (is.na(pubchem_cids[1])) { + message("Query ", identifier, " did not give results at PubChem") + } else { + message("Found ", length(pubchem_cids), " entries in PubChem, using the first one.") + self$get_pubchem(pubchem_cids[1]) + } }, get_pubchem = function(pubchem_cid) { - self$pubchem = webchem::cid_compinfo(pubchem_cid) + self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid")) + self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]] + + self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSMILES - self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSmiles - if (self$pubchem$IsomericSmiles != self$pubchem$CanonicalSmiles) { - self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSmiles + if (self$pubchem$IsomericSMILES != self$pubchem$CanonicalSMILES) { + self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSMILES } self$mw = as.numeric(self$pubchem$MolecularWeight) @@ -119,18 +123,20 @@ chent <- R6Class("chent", } }, get_rdkit = function() { + if (!requireNamespace("PythonInR")) + stop("PythonInR can not be loaded") id <- names(self$identifier) - if (!pyIsConnected()) { - pyConnect() + if (!PythonInR::pyIsConnected()) { + PythonInR::pyConnect() } - try_rdkit <- try(pyImport("Chem", from = "rdkit")) + try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit")) if (inherits(try_rdkit, "try-error")) { message("Could not import RDKit in Python session") } else { self$rdkit <- list() - pyImport("Descriptors", from = "rdkit.Chem") - pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')")) - self$rdkit$mw <- pyExecg("mw = Descriptors.MolWt(mol)", "mw") + PythonInR::pyImport("Descriptors", from = "rdkit.Chem") + PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')")) + self$rdkit$mw <- PythonInR::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) @@ -139,11 +145,11 @@ chent <- R6Class("chent", } # Create a grImport Picture - pyImport("Draw", from = "rdkit.Chem") + PythonInR::pyImport("Draw", from = "rdkit.Chem") psfile <- tempfile(fileext = ".ps") xmlfile <- tempfile(fileext = ".xml") cmd <- paste0("Draw.MolToFile(mol, '", psfile, "')") - pyExec(cmd) + PythonInR::pyExec(cmd) PostScriptTrace(psfile, outfilename = xmlfile) unlink(paste0("capture", basename(psfile))) self$Picture <- readPicture(xmlfile) @@ -209,7 +215,8 @@ chent <- R6Class("chent", max_occurrence = max_occurrence, comment = comment, source = source, - pages = pages)) + pages = pages, + stringsAsFactors = FALSE)) }, soil_degradation_endpoints = data.frame(destination = character(0), DT50 = numeric(0), @@ -223,6 +230,17 @@ chent <- R6Class("chent", self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- c(destination, comment, pages) self$soil_degradation_endpoints[i, "DT50"] <- DT50 + }, + ff = data.frame(from = character(0), to = character(0), ff = numeric(0), + comment = character(0), pages = character(0), + stringsAsFactors = FALSE), + add_ff = function(from = "parent", to, ff = 1, comment = "", pages = NA) { + i <- nrow(self$ff) + 1 + if (from != "parent") { + if (!exists(from, self$TPs)) stop(from, " was not found in TPs") + } + if (!exists(to, self$TPs)) stop(to, " was not found in TPs") + self$ff[i, ] <- c(from, to, ff, comment, pages) } ) ) @@ -231,6 +249,7 @@ chent <- R6Class("chent", #' #' @param x The chent object to be printed #' @param ... Further arguments for compatibility with the S3 method +#' @importFrom utils head #' @export print.chent = function(x, ...) { cat("<chent>\n") @@ -239,15 +258,14 @@ print.chent = function(x, ...) { cat ("SMILES string $smiles:\n") print(x$smiles) if (!is.null(x$mw)) cat ("Molecular weight $mw:", round(x$mw, 1), "\n") - if (!is.null(x$pubchem)) { - cat ("PubChem synonyms (first 10):\n") + if (!is.null(x$pubchem$synonyms)) { + cat ("PubChem synonyms (up to 10):\n") print(head(x$pubchem$synonyms, n = 10L)) } } #' Draw SVG graph from a chent object using RDKit #' -#' @importFrom PythonInR pyIsConnected pyConnect pyImport pyExec #' @param x The chent object to be plotted #' @param width The desired width in pixels #' @param height The desired height in pixels @@ -257,19 +275,19 @@ print.chent = function(x, ...) { draw_svg.chent = function(x, width = 300, height = 150, filename = paste0(names(x$identifier), ".svg"), subdir = "svg") { - if (!pyIsConnected()) { - pyConnect() + if (!PythonInR::pyIsConnected()) { + PythonInR::pyConnect() } - try_rdkit <- try(pyImport("Chem", from = "rdkit")) + try_rdkit <- try(PythonInR::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$smiles, "')")) - pyImport("Draw", from = "rdkit.Chem") + PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", x$smiles, "')")) + PythonInR::pyImport("Draw", from = "rdkit.Chem") cmd <- paste0("Draw.MolToFile(mol, '", file.path(subdir, filename), "', size = (", width, ", ", height, "))") - pyExec(cmd) + PythonInR::pyExec(cmd) } } @@ -309,7 +327,7 @@ pai <- R6Class("pai", if (!missing(iso) & alanwood) { message("alanwood.net:") - self$alanwood = webchem::alanwood(identifier, type = "commonname") + self$alanwood = webchem::aw_query(identifier, type = "commonname")[[1]] if (is.na(self$alanwood[1])) { message("Common name ", identifier, " is not known at www.alanwood.net, trying PubChem") } else { @@ -320,6 +338,7 @@ pai <- R6Class("pai", attr(self$inchikey, "source") <- "alanwood" } } + super$initialize(identifier = identifier, smiles = smiles, pubchem = pubchem, rdkit = rdkit, chyaml = chyaml) |