diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 484 | ||||
| -rw-r--r-- | R/zzz.R | 10 |
2 files changed, 346 insertions, 148 deletions
@@ -1,87 +1,111 @@ -# 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 <http://www.gnu.org/licenses/> - -#' An R6 class for chemical entities with associated data +#' @title 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. +#' @description 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 utils URLencode #' @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 <rdkit.Chem.rdchem.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 +#' @param identifier Identifier to be stored in the object +#' @param smiles Optional user provided SMILES code +#' @param inchikey Optional user provided InChI Key +#' @param pubchem Should an attempt be made to retrieve chemical +#' information from PubChem via the webchem package? +#' @param pubchem_from Possibility to select the argument +#' that is used to query pubchem +#' @param rdkit Should an attempt be made to retrieve chemical +#' information from a local rdkit installation via python +#' and the reticulate package? +#' @param template An optional SMILES code to be used as template for RDKit +#' @param chyaml Should we look for a identifier.yaml file in the working +#' directory? +#' @param T Temperature +#' @param pH pH value +#' @param source An acronym specifying the source of the information +#' @param page The page from which the information was taken +#' @param soils Names of the soils +#' @param type The soil type +#' @param pH_orig The pH stated in the study +#' @param pH_medium The medium in which this pH was measured +#' @param pH_H2O The pH extrapolated to pure water +#' @param perc_OC The percentage of organic carbon in the soil +#' @param pages The pages from which the information was taken +#' @param remark A remark +#' @param file The file to write to +#' @param dir The directory to write the file to #' @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) #' } - +#' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) +#' print(oct) chent <- R6Class("chent", - public <- list( + public = list( + #' @field identifier (`character(1)`)\cr + #' The identifier that was used to initiate the object, with attribute 'source' identifier = NULL, + + #' @field inchikey (`character(1)`)\cr + #' InChI Key, with attribute 'source' inchikey = NULL, + + #' @field smiles (`character()`)\cr + #' SMILES code(s), with attribute 'source' smiles = NULL, + + #' @field mw (`numeric(1)`)\cr + #' Molecular weight, with attribute 'source' mw = NULL, + + #' @field pubchem (`list()`)\cr + #' List of information retrieved from PubChem pubchem = NULL, + + #' @field rdkit + #' List of information obtained with RDKit rdkit = NULL, + + #' @field mol <rdkit.Chem.rdchem.Mol> object mol = NULL, + + #' @field svg SVG code svg = NULL, + + #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport Picture = NULL, + + #' @field Pict_font_size Font size as extracted from the intermediate PostScript file Pict_font_size = NULL, + + #' @field pdf_height Height of the MediaBox in the pdf after cropping pdf_height = NULL, + + #' @field p0 Vapour pressure in Pa p0 = NULL, + + #' @field cwsat Water solubility in mg/L cwsat = NULL, + + #' @field PUF Plant uptake factor PUF = NULL, + + #' @field chyaml List of information obtained from a YAML file chyaml = NULL, - initialize = function(identifier, smiles = NULL, smiles_source = 'user', - inchikey = NULL, inchikey_source = 'user', - pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), - rdkit = TRUE, template = NULL, - chyaml = TRUE) { + + #' @description + #' Creates a new instance of this [R6][R6::R6Class] class. + initialize = function(identifier, smiles = NULL, inchikey = NULL, + pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), + rdkit = TRUE, template = NULL, + chyaml = FALSE) { self$identifier <- identifier names(self$identifier) <- make.names(identifier) @@ -103,9 +127,14 @@ chent <- R6Class("chent", if (is.null(self$smiles)) { message("RDKit would need a SMILES code") } else { + available_smiles <- names(self$smiles) + smiles_preference <- c("user", "PubChem_Isomeric", "PubChem_Canonical") + smiles_preferred_i <- min(match(available_smiles, smiles_preference)) + smiles_preferred <- smiles_preference[smiles_preferred_i] + message("Trying to get chemical information from RDKit using ", - names(self$smiles)[1], " SMILES\n", - self$smiles[1]) + smiles_preferred, " SMILES\n", + self$smiles[smiles_preferred]) self$get_rdkit(template = template) self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit" @@ -118,8 +147,28 @@ chent <- R6Class("chent", if (chyaml) { self$get_chyaml() } + + # Define main identifiers as NA if still not available + if (is.null(self$smiles)) { + self$smiles <- NA + attr(self$smiles, "source") <- "user" + } + if (is.null(self$inchikey)) { + self$inchikey<- NA + attr(self$inchikey, "source") <- "user" + } + if (is.null(self$mw)) { + self$mw<- NA + attr(self$mw, "source") <- "user" + } + invisible(self) }, + + #' @description + #' Try to get chemical information from PubChem + #' @param query Query string to be passed to [get_cid][webchem::get_cid] + #' @param from Passed to [get_cid][webchem::get_cid] try_pubchem = function(query, from = 'name') { message("PubChem:") if (missing(query)) query <- self$identifier @@ -131,6 +180,10 @@ chent <- R6Class("chent", self$get_pubchem(pubchem_result[[1, "cid"]]) } }, + + #' @description + #' Get chemical information from PubChem for a known PubChem CID + #' @param pubchem_cid CID get_pubchem = function(pubchem_cid) { self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid", properties = c("MolecularFormula", "MolecularWeight", @@ -153,25 +206,34 @@ chent <- R6Class("chent", self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" } else { - if (length(self$inchikey) > 1) { - message("InChIKey ", self$inchikey, " retreived from ", - attr(self$inchikey, "source"), - " has length > 1, using PubChem InChIKey") + if (is.na(self$inchikey)) { + warning("Overwriting uninitialized 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$inchikey, "source")) + if (length(self$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 { - attr(self$inchikey, "source") <- c(attr(self$inchikey, "source"), "pubchem") + 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$inchikey, "source"), "pubchem") + } } } } }, + + #' @description + #' Get chemical information from RDKit if available get_rdkit = function(template = NULL) { - if(!rdkit_available) { + if (!rdkit_available) { stop("RDKit is not available") } self$rdkit <- list() @@ -212,11 +274,20 @@ chent <- R6Class("chent", self$Picture <- readPicture(xmlfile) unlink(c(xmlfile, psfile, svgfile)) }, + + #' @description + #' Obtain information from a YAML file + #' @param repo Should the file be looked for in the current working + #' directory, a local git repository under `~/git/chyaml`, or from + #' the web (not implemented). + #' @param chyaml The filename to be looked for get_chyaml = function(repo = c("wd", "local", "web"), - chyaml = paste0(URLencode(self$identifier), ".yaml")) { + chyaml = paste0(URLencode(self$identifier), ".yaml")) + { repo = match.arg(repo) - paths = c(wd = ".", - local = file.path("~", "git/chyaml")) + paths = c( + wd = ".", + local = file.path("~", "git/chyaml")) chyaml_handlers = list( expr = function(x) NULL, # To avoid security risks from reading chyaml files @@ -240,6 +311,10 @@ chent <- R6Class("chent", message("web repositories not implemented") } }, + + #' @description + #' Add a vapour pressure + #' @param p0 The vapour pressure in Pa add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { self$p0 <- p0 attr(self$p0, "T") <- T @@ -247,7 +322,13 @@ chent <- R6Class("chent", attr(self$p0, "page") <- page attr(self$p0, "remark") <- remark }, - add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") { + + #' @description + #' Add a water solubility + #' @param cwsat The water solubility in mg/L + add_cwsat = function(cwsat, T = NA, pH = NA, + source = NA, page = NA, remark = "") + { self$cwsat <- cwsat attr(self$cwsat, "T") <- T attr(self$cwsat, "pH") <- pH @@ -255,31 +336,57 @@ chent <- R6Class("chent", 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") { + + #' @description + #' Add a plant uptake factor + #' @param PUF The plant uptake factor, a number between 0 and 1 + 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 }, + + #' @field TPs List of transformation products as chent objects TPs = list(), + + #' @description + #' Add a transformation product to the internal list + #' @param x A [chent] object, or an identifier to generate a [chent] object + #' @param pubchem Should chemical information be obtained from PubChem? 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) + chent <- chent$new(x, smiles = smiles, pubchem = pubchem) } self$TPs[[id]] <- chent }, + + #' @field transformations Data frame of observed transformations transformations = data.frame(study_type = character(0), - TP_identifier = character(0), - max_occurrence = numeric(0), - source = character(0), - pages = character(0), - stringsAsFactors = FALSE), + TP_identifier = character(0), + max_occurrence = numeric(0), + source = character(0), + page = character(0), + stringsAsFactors = FALSE), + + #' @description + #' Add a line in the internal dataframe holding observed transformations + #' @param study_type A characterisation of the study type + #' @param TP_identifier An identifier of one of the transformation products + #' in `self$TPs` + #' @param max_occurrence The maximum observed occurrence of the + #' transformation product, expressed as a fraction of the amount that would + #' result from stochiometric transformation add_transformation = function(study_type, TP_identifier, max_occurrence, - remark = "", source = NA, pages = NA) { + remark = "", source = NA, pages = NA) + { TP_name = make.names(TP_identifier) if (!inherits(self$TPs[[TP_name]], "chent")) { stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()")) @@ -288,23 +395,41 @@ chent <- R6Class("chent", if (is.numeric(pages)) pages <- paste(pages, collapse = ", ") cn <- colnames(self$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)) + data.frame(study_type = study_type, + TP_identifier = TP_identifier, + max_occurrence = max_occurrence, + remark = remark, + source = source, + page = page, + stringsAsFactors = FALSE)) }, + + #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, + + #' @description + #' Add a line in the internal dataframe holding modelling DT50 values + #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide + #' fate modelling + #' @param DT50_mod_ref The normalised modelling DT50 in the sense of + #' regulatory pesticide fate modelling + #' @param country The country (mainly for field studies) + #' @param temperature The temperature during the study in degrees Celsius + #' @param moisture The moisture during the study + #' @param category Is it a laboratory ('lab') or field study ('field') + #' @param formulation Name of the formulation applied, if it was not + #' the technical active ingredient + #' @param model The degradation model used for deriving `DT50_mod` + #' @param chi2 The relative error as defined in FOCUS kinetics 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) { + 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, @@ -331,10 +456,21 @@ chent <- R6Class("chent", self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation) } }, + + #' @field soil_ff Dataframe of formation fractions soil_ff = NULL, - add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) { + + #' @description + #' Add one or more formation fractions for degradation in soil + #' @param target The identifier(s) of the transformation product + #' @param soils The soil name(s) in which the transformation was observed + #' @param ff The formation fraction(s) + add_soil_ff = function(target, soils, ff = 1, + remark = "", source, page = NA) + { new_soil_ff = data.frame( target = target, + target = target, soil = soils, ff = ff, remark = remark, @@ -347,13 +483,25 @@ chent <- R6Class("chent", self$soil_ff <- rbind(self$soil_ff, new_soil_ff) } }, + + #' @field soil_sorption Dataframe of soil sorption data 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) { + + #' @description + #' Add soil sorption data + #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) + #' or according to Freundlich + #' @param Kfoc The constant from above, normalised to soil organic carbon + #' @param N The Freundlich exponent + #' @param perc_clay The percentage of clay in the soil + #' @param CEC The cation exchange capacity + 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, @@ -372,8 +520,11 @@ chent <- R6Class("chent", self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption) } }, - pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", - template = NULL) { + + #' @description + #' Write a PDF image of the structure + pdf = function(file = paste0(self$identifier, ".pdf"), + dir = "structures/pdf", template = NULL) { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") @@ -393,8 +544,13 @@ chent <- R6Class("chent", 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') { + + #' @description + #' Write a PNG image of the structure + #' @param antialias Passed to [png][grDevices::png] + png = function(file = paste0(self$identifier, ".png"), + dir = "structures/png", antialias = 'gray') + { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") @@ -406,7 +562,12 @@ chent <- R6Class("chent", plot(self) dev.off() }, - emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") { + + #' @description + #' Write an EMF image of the structure using [emf][devEMF::emf] + emf = function(file = paste0(self$identifier, ".emf"), + dir = "structures/emf") + { if (!requireNamespace("devEMF")) { stop("You need to have the devEMF package installed for this function") } @@ -452,8 +613,8 @@ print.chent = function(x, ...) { #' @param subdir The path to which the file should be written #' @export draw_svg.chent = function(x, width = 300, height = 150, - filename = paste0(names(x$identifier), ".svg"), - subdir = "svg") { + filename = paste0(names(x$identifier), ".svg"), + subdir = "svg") { if (!rdkit_available) { stop("RDkit is not available via reticulate") } else { @@ -482,18 +643,16 @@ plot.chent = function(x, ...) { grid.picture(x$Picture) } -#' An R6 class for pesticidal active ingredients and associated data +#' @title 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. +#' @description This class is derived from [chent]. It makes it easy +#' to create a [chent] from the ISO common name of a pesticide active +#' ingredient, and additionally stores the ISO name as well as +#' the complete result of querying the BCPC compendium using +#' [bcpc_query][webchem::bcpc_query]. #' -#' @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, @@ -507,19 +666,39 @@ plot.chent = function(x, ...) { #' } #' #' } - pai <- R6Class("pai", inherit = chent, - public <- list( + public = list( + + #' @field iso ISO common name of the active ingredient according to ISO 1750 iso = NULL, + + #' @field bcpc Information retrieved from the BCPC compendium available online + #' at <pesticidecompendium.bcpc.org> bcpc = NULL, + + #' @description + #' Create a new pai object + #' @param iso The ISO common name to be used in the query of the + #' BCPC compendium + #' @param identifier Alternative identifier used for querying pubchem + #' @param smiles Optional user provided SMILES code + #' @param inchikey Optional user provided InChI Key + #' @param bcpc Should the BCPC compendium be queried? + #' @param pubchem Should an attempt be made to retrieve chemical + #' information from PubChem via the webchem package? + #' @param pubchem_from Possibility to select the argument + #' that is used to query pubchem + #' @param rdkit Should an attempt be made to retrieve chemical + #' information from a local rdkit installation via python + #' and the reticulate package? + #' @param template An optional SMILES code to be used as template for RDKit + #' @param chyaml Should we look for a identifier.yaml file in the working 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) + smiles = NULL, inchikey = NULL, bcpc = TRUE, + pubchem = TRUE, pubchem_from = 'auto', + rdkit = TRUE, template = NULL, + chyaml = FALSE) { if (!is.null(inchikey)) { @@ -540,9 +719,9 @@ pai <- R6Class("pai", 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 (length(bcpc_ik) == 1 && !is.na(bcpc_ik)) { if (is.null(self$inchikey)) { - self$inchikey = self$bcpc$inchikey + self$inchikey = substr(self$bcpc$inchikey, 1, 27) attr(self$inchikey, "source") <- "bcpc" } else { if (bcpc_ik == self$inchikey) { @@ -564,10 +743,9 @@ pai <- R6Class("pai", } super$initialize(identifier = identifier, - smiles = smiles, smiles_source = smiles_source, - inchikey = self$inchikey, - pubchem = pubchem, pubchem_from = pubchem_from, - rdkit = rdkit, template = template, chyaml = chyaml) + smiles = smiles, inchikey = self$inchikey, + pubchem = pubchem, pubchem_from = pubchem_from, + rdkit = rdkit, template = template, chyaml = chyaml) invisible(self) } @@ -592,30 +770,45 @@ print.pai = function(x, ...) { } } -#' R6 class for holding a product with at least one active ingredient +#' @title R6 class for a plant protection product with at least one active ingredient #' -#' An R6 class for holding information about a product with at least one active ingredient +#' @description Contains basic information about the active ingredients in the +#' product #' -#' @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( +ppp <- R6Class("ppp", + public = list( + + #' @field name The name of the product name = NULL, + + #' @field ais A list of active ingredients ais = list(), + + #' @field concentrations The concentration of the ais concentrations = NULL, + + #' @field concentration_units Defaults to g/L concentration_units = NULL, + + #' @field density The density of the product density = NULL, + + #' @field density_units Defaults to g/L density_units = "g/L", + + #' @description + #' Creates a new instance of this [R6][R6::R6Class] class. + #' @param name The name of the product + #' @param ... Identifiers of the active ingredients + #' @param concentrations Concentrations of the active ingredients + #' @param concentration_units Defaults to g/L + #' @param density The density + #' @param density_units Defaults to g/L initialize = function(name, ..., concentrations, concentration_units = "g/L", - density = 1000, density_units = "g/L") { + density = 1000, density_units = "g/L") + { self$name <- name self$ais <- list(...) self$concentrations <- concentrations @@ -623,11 +816,16 @@ pp <- R6Class("pp", self$density_units <- density_units names(self$concentrations) <- names(self$ais) self$concentration_units <- concentration_units - }, - print = function() { - cat("<pp> named", self$name, "\n") } ) ) +#' Printing method for ppp objects (plant protection products) +#' +#' @param x The chent object to be printed +#' @param ... Further arguments for compatibility with the S3 method +#' @export +print.ppp = function(x, ...) { + cat("<pp> named", x$name, "\n") +} # vim: set ts=2 sw=2 expandtab: @@ -1,9 +1,9 @@ .onLoad = function(libname, pkgname) { - rdkit_available <- FALSE - rdkit_module <- try(reticulate::import("rdkit"), silent = TRUE) - if (!inherits(rdkit_module, "try-error")) { - rdkit_available <- TRUE - } + conf <- reticulate::py_discover_config("rdkit") + rdkit_available <- reticulate::py_module_available("rdkit") + rdkit_module <- try( + reticulate::import("rdkit"), + silent = TRUE) assign('rdkit_available', rdkit_available, envir = topenv()) assign('rdkit_module', rdkit_module, envir = topenv()) } |