From 816de01ce642c1c3d633ffb1cbcf960036d27114 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Fri, 10 Nov 2023 18:40:34 +0100 Subject: Make an RStudio project and improve the docs --- R/chent.R | 201 +++++++++++++++++++++++++++++++++++++++++--------------------- 1 file changed, 134 insertions(+), 67 deletions(-) (limited to 'R') diff --git a/R/chent.R b/R/chent.R index c89efec..dc9be6f 100644 --- a/R/chent.R +++ b/R/chent.R @@ -1,25 +1,8 @@ -# 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 +#' @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 @@ -28,27 +11,8 @@ #' @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$new("1-octanol", smiles = "CCCCCCCCO") +#' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) #' print(oct) #' if (!is.null(oct$Picture)) { #' plot(oct) @@ -59,30 +23,80 @@ #' if (!is.null(caffeine$Picture)) { #' plot(caffeine) #' } - 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 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. + #' + #' @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? + initialize = function(identifier, smiles = NULL, inchikey = NULL, + 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) @@ -120,6 +134,10 @@ chent <- R6Class("chent", } invisible(self) }, + + #' 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$identifier @@ -131,6 +149,9 @@ chent <- R6Class("chent", self$get_pubchem(pubchem_result[[1, "cid"]]) } }, + + #' Get chemical information from PubChem for a known PubChem CID + #' @param pubchem_cid CID get_pubchem = function(pubchem_cid) { self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid", properties = c("MolecularFormula", "MolecularWeight", @@ -170,6 +191,9 @@ chent <- R6Class("chent", } } }, + + #' Get chemical information from RDKit if available + #' @param template Optional template specified as a SMILES code get_rdkit = function(template = NULL) { if(!rdkit_available) { stop("RDKit is not available") @@ -212,11 +236,18 @@ chent <- R6Class("chent", self$Picture <- readPicture(xmlfile) unlink(c(xmlfile, psfile, svgfile)) }, + + #' 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). 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 +271,13 @@ chent <- R6Class("chent", message("web repositories not implemented") } }, + + #' Add a vapour pressure + #' @param p0 The vapour pressure in Pa + #' @param T Temperature + #' @param source An acronym specifying the source of the information + #' @param page The page from which the information was taken + #' @param remark A remark add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { self$p0 <- p0 attr(self$p0, "T") <- T @@ -247,6 +285,9 @@ chent <- R6Class("chent", attr(self$p0, "page") <- page attr(self$p0, "remark") <- remark }, + + #' Add a water solubility + #' @param p0 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 @@ -255,13 +296,23 @@ chent <- R6Class("chent", attr(self$cwsat, "page") <- page attr(self$cwsat, "remark") <- remark }, + + #' 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(), + + #' Add a transformation product to the internal list + #' @param x A [chent] object, or an identifier to generate a [chent] object + #' @param smiles A SMILES code for defining 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$identifier) @@ -272,14 +323,19 @@ chent <- R6Class("chent", } self$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), + + #' Add a line in the internal dataframe holding observed transformations 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()")) @@ -296,15 +352,20 @@ chent <- R6Class("chent", pages = pages, stringsAsFactors = FALSE)) }, + + #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, + + #' Add a line in the internal dataframe holding modelling DT50 values 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, @@ -331,9 +392,13 @@ 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) { new_soil_ff = data.frame( + target = target, target = target, soil = soils, ff = ff, @@ -347,7 +412,10 @@ 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, @@ -372,8 +440,9 @@ chent <- R6Class("chent", self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption) } }, - pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", - template = NULL) { + + pdf = function(file = paste0(self$identifier, ".pdf"), + dir = "structures/pdf", template = NULL) { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") @@ -493,7 +562,6 @@ plot.chent = function(x, ...) { #' @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, @@ -507,15 +575,14 @@ plot.chent = function(x, ...) { #' } #' #' } - 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', + smiles = NULL, + inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = 'auto', rdkit = TRUE, template = NULL, @@ -564,7 +631,7 @@ pai <- R6Class("pai", } super$initialize(identifier = identifier, - smiles = smiles, smiles_source = smiles_source, + smiles = smiles, inchikey = self$inchikey, pubchem = pubchem, pubchem_from = pubchem_from, rdkit = rdkit, template = template, chyaml = chyaml) -- cgit v1.2.1