# Copyright (C) 2016-2021 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package chents # This program is free software: you can redistribute it and/or modify it under # the terms of the GNU General Public License as published by the Free Software # Foundation, either version 3 of the License, or (at your option) any later # version. # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more # details. # You should have received a copy of the GNU General Public License along with # this program. If not, see #' An R6 class for chemical entities with associated data #' #' 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. #' #' @export #' @format An \code{\link{R6Class}} generator object #' @importFrom R6 R6Class #' @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' #' @field mw Molecular weight, with attribute 'source' #' @field pubchem List of information retreived from PubChem #' @field rdkit List of information obtained with RDKit #' @field mol object #' @field svg SVG code #' @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 p0 Vapour pressure in Pa #' @field cwsat Water solubility in mg/L #' @field chyaml List of information obtained from a YAML file #' @field soil_degradation Dataframe of modelling DT50 values #' @field soil_ff Dataframe of formation fractions #' @field soil_sorption Dataframe of soil sorption data #' @field PUF Plant uptake factor #' @keywords data #' @examples #' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") #' print(oct) #' if (!is.null(oct$Picture)) { #' plot(oct) #' } #' #' caffeine <- chent$new("caffeine") #' print(caffeine) #' if (!is.null(caffeine$Picture)) { #' plot(caffeine) #' } chent <- R6Class("chent", public <- list( identifier = NULL, inchikey = NULL, smiles = NULL, mw = NULL, pubchem = NULL, rdkit = NULL, mol = NULL, svg = NULL, Picture = NULL, Pict_font_size = NULL, pdf_height = NULL, p0 = NULL, cwsat = NULL, PUF = NULL, chyaml = NULL, initialize = function(identifier, smiles = NULL, smiles_source = 'user', inchikey = NULL, inchikey_source = 'user', pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), rdkit = TRUE, template = NULL, chyaml = TRUE) { self$identifier <- identifier names(self$identifier) <- make.names(identifier) pubchem_from = match.arg(pubchem_from) self$smiles <- c(user = smiles) if (pubchem) { if (pubchem_from == 'name') { query = identifier } else { query = get(pubchem_from) } self$try_pubchem(query, from = pubchem_from) } if (rdkit) { if(rdkit_available) { if (is.null(self$smiles)) { message("RDKit would need a SMILES code") } else { message("Trying to get chemical information from RDKit using ", names(self$smiles)[1], " SMILES\n", self$smiles[1]) self$get_rdkit(template = template) self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit" } } else { message("RDKit is not available") } } if (chyaml) { self$get_chyaml() } invisible(self) }, try_pubchem = function(query, from = 'name') { message("PubChem:") if (missing(query)) query <- self$identifier pubchem_result = webchem::get_cid(query, from = from, match = "first") if (is.na(pubchem_result[[1, "cid"]])) { message("Query ", query, " did not give results at PubChem") } else { self$get_pubchem(pubchem_result[[1, "cid"]]) } }, get_pubchem = function(pubchem_cid) { self$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$CanonicalSMILES if (self$pubchem$IsomericSMILES != self$pubchem$CanonicalSMILES) { self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSMILES } self$mw = as.numeric(self$pubchem$MolecularWeight) attr(self$mw, "source") <- "pubchem" if (is.null(self$inchikey)) { self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" } else { if (length(self$inchikey) > 1) { message("InChIKey ", self$inchikey, " retreived from ", attr(self$inchikey, "source"), " has length > 1, using PubChem InChIKey") self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" } else { if (self$pubchem$InChIKey != self$inchikey) { message("InChiKey ", self$pubchem$InChIKey, " from PubChem record does not match\n", "InChiKey ", self$inchikey, " retreived from ", attr(self$inchikey, "source")) } else { attr(self$inchikey, "source") <- c(attr(self$inchikey, "source"), "pubchem") } } } }, get_rdkit = function(template = NULL) { if(!rdkit_available) { stop("RDKit is not available") } self$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$mw)) { if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { message("RDKit mw is ", self$rdkit$mw) message("mw is ", self$mw) } } # Create an SVG representation rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol) if (!is.null(template)) { rdkit_template <- rdkit_module$Chem$MolFromSmiles(template) rdkit_module$Chem$rdDepictor$Compute2DCoords(template) rdkit$Chem$AllChem$GenerateDepictionMatching2DStructure(self$mol, template) } d2d <- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L) d2d$DrawMolecule(self$mol) d2d$FinishDrawing() self$svg <- d2d$GetDrawingText() svgfile <- tempfile(fileext = ".svg") psfile <- tempfile(fileext = ".ps") writeLines(self$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$identifier), ".yaml")) { repo = match.arg(repo) paths = c(wd = ".", local = file.path("~", "git/chyaml")) chyaml_handlers = list( expr = function(x) NULL, # To avoid security risks from reading chyaml files dataframe = function(x) eval(parse(text = paste0("data.frame(", x, ", stringsAsFactors = FALSE)")))) if (repo %in% c("wd", "local")) { path = paths[repo] full = file.path(path, chyaml) if (!file.exists(full)) { message("Did not find chyaml file ", full) } else { if (is(try(self$chyaml <- yaml.load_file(chyaml, handlers = chyaml_handlers)), "try-error")) { message("Could not load ", full) } else { message("Loaded ", full) } } } else { message("web repositories not implemented") } }, add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { self$p0 <- p0 attr(self$p0, "T") <- T attr(self$p0, "source") <- source attr(self$p0, "page") <- page attr(self$p0, "remark") <- remark }, add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") { self$cwsat <- cwsat attr(self$cwsat, "T") <- T attr(self$cwsat, "pH") <- pH attr(self$cwsat, "source") <- source attr(self$cwsat, "page") <- page attr(self$cwsat, "remark") <- remark }, add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") { self$PUF <- PUF attr(self$PUF, "source") <- source attr(self$PUF, "page") <- page attr(self$PUF, "remark") <- remark }, TPs = list(), add_TP = function(x, smiles = NULL, pubchem = FALSE) { if (inherits(x, "chent")) { id <- names(x$identifier) chent <- x } else { id <- make.names(x) chent <- chent$new(x, smiles, pubchem = pubchem) } self$TPs[[id]] <- chent }, transformations = data.frame(study_type = character(0), TP_identifier = character(0), max_occurrence = numeric(0), source = character(0), pages = character(0), stringsAsFactors = FALSE), add_transformation = function(study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA) { TP_name = make.names(TP_identifier) if (!inherits(self$TPs[[TP_name]], "chent")) { stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()")) } TP_chent <- self$TPs[TP_name] if (is.numeric(pages)) pages <- paste(pages, collapse = ", ") cn <- colnames(self$transformations) self$transformations <- rbind(self$transformations, data.frame(study_type = study_type, TP_identifier = TP_identifier, max_occurrence = max_occurrence, remark = remark, source = source, pages = pages, stringsAsFactors = FALSE)) }, soil_degradation = NULL, add_soil_degradation = function(soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, temperature = NA, moisture = NA, category = "lab", formulation = NA, model = NA, chi2 = NA, remark = "", source, page = NA) { new_soil_degradation = data.frame( soil = soils, DT50_mod = DT50_mod, DT50_mod_ref = DT50_mod_ref, type = type, country = country, pH_orig = pH_orig, pH_medium = pH_medium, pH_H2O = pH_H2O, perc_OC = perc_OC, temperature = temperature, moisture = moisture, category = category, formulation = formulation, model = model, chi2 = chi2, remark = remark, source = source, page = page, stringsAsFactors = FALSE) if (is.null(self$soil_degradation)) { self$soil_degradation <- new_soil_degradation } else { self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation) } }, soil_ff = NULL, add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) { new_soil_ff = data.frame( target = target, soil = soils, ff = ff, remark = remark, source = source, page = page, stringsAsFactors = FALSE) if (is.null(self$soil_ff)) { self$soil_ff <- new_soil_ff } else { self$soil_ff <- rbind(self$soil_ff, new_soil_ff) } }, soil_sorption = NULL, add_soil_sorption = function(soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, perc_clay = NA, CEC = NA, remark = "", source, page = NA) { new_soil_sorption = data.frame( soils = soils, Kf = Kf, Kfoc = Kfoc, N = N, type = type, pH_orig = pH_orig, pH_medium = pH_medium, pH_H2O = pH_H2O, perc_OC = perc_OC, perc_clay = perc_clay, CEC = CEC, remark = remark, source = source, page = page, stringsAsFactors = FALSE) if (is.null(self$soil_sorption)) { self$soil_sorption <- new_soil_sorption } else { self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption) } }, pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL) { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") dir.create(dir, recursive = TRUE) } path = file.path(dir, file) message("Creating file '", path, "'") pdf(path) plot(self) dev.off() message("Cropping file '", path, "' using pdfcrop") bash_path <- shQuote(path) system(paste("pdfcrop --margin 10", bash_path, bash_path, "> /dev/null")) # Get the height of the MediaBox head <- readLines(path, n = 20, skipNul = TRUE) m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE)) self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) }, png = function(file = paste0(self$identifier, ".png"), dir = "structures/png", antialias = 'gray') { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") dir.create(dir, recursive = TRUE) } path = file.path(dir, file) message("Creating file '", path, "'") png(path, antialias = antialias) plot(self) dev.off() }, emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") { if (!requireNamespace("devEMF")) { stop("You need to have the devEMF package installed for this function") } 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, "'") devEMF::emf(path) plot(self) dev.off() } ) ) #' Printing method for chent objects #' #' @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("\n") cat("Identifier $identifier", x$identifier, "\n") cat ("InChI Key $inchikey", x$inchikey, "\n") 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$pubchem$synonyms)) { cat ("PubChem synonyms (up to 10):\n") print(head(x$pubchem$synonyms, n = 10L)) } } #' Draw SVG graph from a chent object using RDKit #' #' @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$identifier), ".svg"), subdir = "svg") { if (!rdkit_available) { stop("RDkit is not available via reticulate") } else { if (!dir.exists(subdir)) dir.create(subdir) mol <- rdkit_module$Chem$MolFromSmiles(x$smiles) rdkit_module$Chem$Draw$MolToFile(mol, file.path(subdir, filename), size = c(as.integer(width), as.integer(height))) } } #' Plot method for chent objects #' #' @importFrom grImport grid.picture #' @param x The chent object to be plotted #' @param ... Further arguments passed to \code{\link{grid.picture}} #' @export #' @examples #' caffeine <- chent$new("caffeine") #' print(caffeine) #' if (!is.null(caffeine$Picture)) { #' plot(caffeine) #' } plot.chent = function(x, ...) { if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?") grid.picture(x$Picture) } #' An R6 class for pesticidal active ingredients and associated data #' #' The class is initialised with an identifier which is generally an ISO common name. #' Additional chemical information is retrieved from the internet if available. #' #' @docType class #' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object #' @field iso ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org #' @field bcpc List of information retrieved from pesticidecompendium.bcpc.org #' @keywords data #' @examples #' # On Travis, we get a certificate validation error, #' # likely because the system (xenial) is so old, #' # therefore don't run this example on Travis #' if (Sys.getenv("TRAVIS") == "") { #' #' atr <- pai$new("atrazine") #' print(atr) #' if (!is.null(atr$Picture)) { #' plot(atr) #' } #' #' } pai <- R6Class("pai", inherit = chent, public <- list( iso = NULL, bcpc = NULL, initialize = function(iso, identifier = iso, smiles = NULL, smiles_source = 'user', inchikey = NULL, inchikey_source = 'user', bcpc = TRUE, pubchem = TRUE, pubchem_from = 'auto', rdkit = TRUE, template = NULL, chyaml = TRUE) { if (!is.null(inchikey)) { self$inchikey = inchikey attr(self$inchikey, "source") <- "user" } if (!missing(iso) & bcpc) { message("BCPC:") bcpc_result = webchem::bcpc_query(identifier, from = "name") # Use first element of list, as we passed a query of length one if (is.na(bcpc_result[[1]][1])) { message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem") } else { self$bcpc = bcpc_result[[1]] self$iso = self$bcpc$cname attr(self$iso, "source") <- "bcpc" attr(self$iso, "status") <- self$bcpc$status bcpc_ik = self$bcpc$inchikey if (length(bcpc_ik) == 1 && nchar(bcpc_ik) == 27 && !is.na(bcpc_ik)) { if (is.null(self$inchikey)) { self$inchikey = self$bcpc$inchikey attr(self$inchikey, "source") <- "bcpc" } else { if (bcpc_ik == self$inchikey) { attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc") } else { warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org") } } } } } # Set pubchem_from if not specified if (pubchem_from == 'auto') { pubchem_from = 'name' if (!is.null(self$inchikey)) { pubchem_from = 'inchikey' } } super$initialize(identifier = identifier, smiles = smiles, smiles_source = smiles_source, inchikey = self$inchikey, pubchem = pubchem, pubchem_from = pubchem_from, rdkit = rdkit, template = template, chyaml = chyaml) invisible(self) } ) ) #' Printing method for pai objects (pesticidal active ingredients) #' #' @param x The chent object to be printed #' @param ... Further arguments for compatibility with the S3 method #' @export print.pai = function(x, ...) { cat(" with ISO common name $iso", x$iso, "\n") print.chent(x) if (length(x$TPs) > 0) { cat("\nTransformation products:\n") print(x$TPs) } if (nrow(x$transformations) > 0) { cat("\nTransformations:\n") print(x$transformations) } } #' R6 class for holding a product with at least one active ingredient #' #' An R6 class for holding information about a product with at least one active ingredient #' #' @docType class #' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object. #' @field name The name of the product #' @field ais A list of active ingredients #' @field concentrations The concentration of the ais #' @field concentration_units Defaults to g/L #' @keywords data pp <- R6Class("pp", public <- list( name = NULL, ais = list(), concentrations = NULL, concentration_units = NULL, density = NULL, density_units = "g/L", initialize = function(name, ..., concentrations, concentration_units = "g/L", density = 1000, density_units = "g/L") { self$name <- name self$ais <- list(...) self$concentrations <- concentrations self$density <- density self$density_units <- density_units names(self$concentrations) <- names(self$ais) self$concentration_units <- concentration_units }, print = function() { cat(" named", self$name, "\n") } ) ) # vim: set ts=2 sw=2 expandtab: