From e92727f871c2c8217251e34e52438f18c5f013bb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 22:22:30 +0100 Subject: Import URLencode from utils, rebuild docs This was caught by pkgdown apparently not loading the utils package by default. --- NAMESPACE | 1 + R/chent.R | 123 +++++++++++++++++++++-------------------- docs/pkgdown.yml | 2 +- docs/reference/Rplot001.png | Bin 1011 -> 20412 bytes docs/reference/chent.html | 29 ++++++++-- docs/reference/pai.html | 14 ++++- docs/reference/plot.chent.html | 18 +++++- docs/search.json | 2 +- 8 files changed, 116 insertions(+), 73 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index e56a6c6..4529781 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,6 +12,7 @@ importFrom(grImport,PostScriptTrace) importFrom(grImport,grid.picture) importFrom(grImport,readPicture) importFrom(rsvg,rsvg_ps) +importFrom(utils,URLencode) importFrom(utils,head) importFrom(webchem,cid_compinfo) importFrom(webchem,get_cid) diff --git a/R/chent.R b/R/chent.R index 8a4ad8a..6d18277 100644 --- a/R/chent.R +++ b/R/chent.R @@ -1,12 +1,13 @@ #' @title An R6 class for chemical entities with associated data #' -#' @description The class is initialised with an identifier. Chemical -#' information is retrieved from the internet. Additionally, it can be +#' @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 @@ -29,75 +30,75 @@ chent <- R6Class("chent", #' @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, - + #' @description #' Creates a new instance of this [R6][R6::R6Class] class. - #' - #' @param identifier Identifier to be stored in the object + #' + #' @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 + #' @param pubchem_from Possibility to select the argument #' that is used to query pubchem - #' @param rdkit Should an attempt be made to retrieve chemical + #' @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, + 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) @@ -135,7 +136,7 @@ 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] @@ -150,7 +151,7 @@ chent <- R6Class("chent", self$get_pubchem(pubchem_result[[1, "cid"]]) } }, - + #' Get chemical information from PubChem for a known PubChem CID #' @param pubchem_cid CID get_pubchem = function(pubchem_cid) { @@ -192,7 +193,7 @@ chent <- R6Class("chent", } } }, - + #' Get chemical information from RDKit if available #' @param template Optional template specified as a SMILES code get_rdkit = function(template = NULL) { @@ -237,9 +238,9 @@ chent <- R6Class("chent", self$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 + #' @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 @@ -273,7 +274,7 @@ chent <- R6Class("chent", message("web repositories not implemented") } }, - + #' Add a vapour pressure #' @param p0 The vapour pressure in Pa #' @param T Temperature @@ -287,7 +288,7 @@ chent <- R6Class("chent", attr(self$p0, "page") <- page attr(self$p0, "remark") <- remark }, - + #' Add a water solubility #' @param cwsat The water solubility in mg/L #' @param T Temperature @@ -305,7 +306,7 @@ 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 #' @param source An acronym specifying the source of the information @@ -320,10 +321,10 @@ chent <- R6Class("chent", 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 @@ -338,7 +339,7 @@ chent <- R6Class("chent", } self$TPs[[id]] <- chent }, - + #' @field transformations Data frame of observed transformations transformations = data.frame(study_type = character(0), TP_identifier = character(0), @@ -346,12 +347,12 @@ chent <- R6Class("chent", source = character(0), page = character(0), stringsAsFactors = FALSE), - + #' Add a line in the internal dataframe holding observed transformations #' @param study_type A characterisation of the study type #' @param TP_identifier An identifier of one of the transformation products #' in `self$TPs` - #' @param max_occurrence The maximum observed occurrence of the + #' @param max_occurrence The maximum observed occurrence of the #' transformation product, expressed as a fraction of the amount that would #' result from stochiometric transformation #' @param source An acronym specifying the source of the information @@ -376,10 +377,10 @@ chent <- R6Class("chent", page = page, stringsAsFactors = FALSE)) }, - + #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, - + #' Add a line in the internal dataframe holding modelling DT50 values #' @param soils Names of the soils #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide @@ -395,7 +396,7 @@ chent <- R6Class("chent", #' @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 + #' @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 @@ -437,10 +438,10 @@ chent <- R6Class("chent", self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation) } }, - + #' @field soil_ff Dataframe of formation fractions soil_ff = NULL, - + # 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 @@ -463,12 +464,12 @@ 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 data - #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) + #' @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 @@ -498,9 +499,9 @@ chent <- R6Class("chent", self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption) } }, - + #' Write a PDF image of the structure - #' @param file The file to write to + #' @param file The file to write to #' @param dir The directory to write the file to #' @param template A template expressed as SMILES to use in RDKit pdf = function(file = paste0(self$identifier, ".pdf"), @@ -524,7 +525,7 @@ chent <- R6Class("chent", m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE)) self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) }, - + #' Write a PNG image of the structure #' @param antialias Passed to [png][grDevices::png] png = function(file = paste0(self$identifier, ".png"), @@ -541,7 +542,7 @@ chent <- R6Class("chent", plot(self) dev.off() }, - + #' Write an EMF image of the structure using [emf][devEMF::emf] #' @param file The file to write to emf = function(file = paste0(self$identifier, ".emf"), @@ -649,14 +650,14 @@ plot.chent = function(x, ...) { pai <- R6Class("pai", inherit = chent, 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 bcpc = NULL, - + #' Creates a new instance of this [R6][R6::R6Class] class. #' #' @description This class is derived from [chent]. It makes it easy @@ -664,8 +665,8 @@ pai <- R6Class("pai", #' ingredient, and additionally stores the ISO name as well as #' the complete result of querying the BCPC compendium using #' [bcpc_query][webchem::bcpc_query]. - #' - #' @param iso The ISO common name to be used in the query of the + #' + #' @param iso The ISO common name to be used in the query of the #' BCPC compendium #' #' @param identifier Alternative identifier used for querying pubchem @@ -757,27 +758,27 @@ print.pai = function(x, ...) { 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", - + #' Creates a new instance of this [R6][R6::R6Class] class. - #' + #' #' @field ... Identifiers of the active ingredients #' @field concentrations Concentrations of the active ingredients #' @field concentration_units Defaults to g/L @@ -794,7 +795,7 @@ ppp <- R6Class("ppp", names(self$concentrations) <- names(self$ais) self$concentration_units <- concentration_units }, - + #' Printing method print = function() { cat(" named", self$name, "\n") diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 44cd4ff..26105cf 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-11-12T21:10Z +last_built: 2023-11-12T21:21Z urls: reference: https://pkgdown.jrwb.de/chents/reference article: https://pkgdown.jrwb.de/chents/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 17a3580..0e4970e 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html index cb0b1eb..2cedc00 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -771,25 +771,42 @@ Write an EMF image of the structure using 
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
 #> Trying to get chemical information from RDKit using user SMILES
 #> CCCCCCCCO
-#> Error in URLencode(self$identifier): could not find function "URLencode"
+#> Did not find chyaml file ./1-octanol.yaml
 print(oct)
-#> Error in eval(expr, envir, enclos): object 'oct' not found
+#> <chent>
+#> Identifier $identifier 1-octanol 
+#> InChI Key $inchikey 
+#> SMILES string $smiles:
+#>        user 
+#> "CCCCCCCCO" 
+#> Molecular weight $mw: 130.2 
 if (!is.null(oct$Picture)) {
   plot(oct)
 }
-#> Error in eval(expr, envir, enclos): object 'oct' not found
 
 caffeine <- chent$new("caffeine")
 #> PubChem:
 #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
 #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
-#> Error in URLencode(self$identifier): could not find function "URLencode"
+#> Did not find chyaml file ./caffeine.yaml
 print(caffeine)
-#> Error in eval(expr, envir, enclos): object 'caffeine' not found
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              PubChem_Canonical 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"                
 if (!is.null(caffeine$Picture)) {
   plot(caffeine)
 }
-#> Error in eval(expr, envir, enclos): object 'caffeine' not found
+