diff options
Diffstat (limited to 'R/chent.R')
| -rw-r--r-- | R/chent.R | 141 |
1 files changed, 66 insertions, 75 deletions
@@ -12,6 +12,33 @@ #' @importFrom grImport PostScriptTrace readPicture #' @importFrom yaml yaml.load_file #' @importFrom rsvg rsvg_ps +#' @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$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) #' print(oct) @@ -80,23 +107,10 @@ chent <- R6Class("chent", #' @description #' Creates a new instance of this [R6][R6::R6Class] class. #' - #' @param identifier Identifier to be stored in the object - #' @param smiles Optional user provided SMILES code - #' @param inchikey Optional user provided InChI Key - #' @param pubchem Should an attempt be made to retrieve chemical - #' information from PubChem via the webchem package? - #' @param pubchem_from Possibility to select the argument - #' that is used to query pubchem - #' @param rdkit Should an attempt be made to retrieve chemical - #' information from a local rdkit installation via python - #' and the reticulate package? - #' @param template An optional SMILES code to be used as template for RDKit - #' @param chyaml Should we look for a identifier.yaml file in the working - #' directory? initialize = function(identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), rdkit = TRUE, template = NULL, - chyaml = TRUE) { + chyaml = FALSE) { self$identifier <- identifier names(self$identifier) <- make.names(identifier) @@ -219,8 +233,8 @@ chent <- R6Class("chent", } }, + #' @description #' Get chemical information from RDKit if available - #' @param template Optional template specified as a SMILES code get_rdkit = function(template = NULL) { if (!rdkit_available) { stop("RDKit is not available") @@ -302,10 +316,6 @@ chent <- R6Class("chent", #' Add a vapour pressure #' @param p0 The vapour pressure in Pa - #' @param T Temperature - #' @param source An acronym specifying the source of the information - #' @param page The page from which the information was taken - #' @param remark A remark add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { self$p0 <- p0 attr(self$p0, "T") <- T @@ -316,11 +326,6 @@ chent <- R6Class("chent", #' Add a water solubility #' @param cwsat The water solubility in mg/L - #' @param T Temperature - #' @param pH The pH value - #' @param source An acronym specifying the source of the information - #' @param page The page from which the information was taken - #' @param remark A remark add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") { @@ -334,9 +339,6 @@ chent <- R6Class("chent", #' Add a plant uptake factor #' @param PUF The plant uptake factor, a number between 0 and 1 - #' @param source An acronym specifying the source of the information - #' @param page The page from which the information was taken - #' @param remark A remark add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") @@ -352,7 +354,6 @@ chent <- R6Class("chent", #' Add a transformation product to the internal list #' @param x A [chent] object, or an identifier to generate a [chent] object - #' @param smiles A SMILES code for defining a [chent] object #' @param pubchem Should chemical information be obtained from PubChem? add_TP = function(x, smiles = NULL, pubchem = FALSE) { if (inherits(x, "chent")) { @@ -360,7 +361,7 @@ chent <- R6Class("chent", chent <- x } else { id <- make.names(x) - chent <- chent$new(x, smiles, pubchem = pubchem) + chent <- chent$new(x, smiles = smiles, pubchem = pubchem) } self$TPs[[id]] <- chent }, @@ -380,9 +381,6 @@ chent <- R6Class("chent", #' @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 - #' @param pages The page from which the information was taken - #' @param remark A remark add_transformation = function(study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA) { @@ -407,17 +405,11 @@ chent <- R6Class("chent", 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 #' fate modelling #' @param DT50_mod_ref The normalised modelling DT50 in the sense of #' regulatory pesticide fate modelling - #' @param type The soil type #' @param country The country (mainly for field studies) - #' @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 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') @@ -425,9 +417,6 @@ chent <- R6Class("chent", #' the technical active ingredient #' @param model The degradation model used for deriving `DT50_mod` #' @param chi2 The relative error as defined in FOCUS kinetics - #' @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_soil_degradation = function(soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, @@ -500,7 +489,8 @@ chent <- R6Class("chent", #' @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, + 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, @@ -525,10 +515,8 @@ chent <- R6Class("chent", } }, + #' @description #' Write a PDF image of the structure - #' @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$identifier, ".pdf"), dir = "structures/pdf", template = NULL) { if (!dir.exists(dir)) { @@ -568,8 +556,8 @@ chent <- R6Class("chent", dev.off() }, + #' @description #' Write an EMF image of the structure using [emf][devEMF::emf] - #' @param file The file to write to emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") { @@ -650,12 +638,12 @@ plot.chent = function(x, ...) { #' @title An R6 class for pesticidal active ingredients and associated data #' -#' @description 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 #' @examples @@ -671,7 +659,6 @@ plot.chent = function(x, ...) { #' } #' #' } - pai <- R6Class("pai", inherit = chent, public = list( @@ -683,23 +670,27 @@ pai <- R6Class("pai", #' at <pesticidecompendium.bcpc.org> bcpc = NULL, - #' Creates a new instance of this [R6][R6::R6Class] class. - #' - #' @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]. - #' #' @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, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = 'auto', rdkit = TRUE, template = NULL, - chyaml = TRUE) + chyaml = FALSE) { if (!is.null(inchikey)) { @@ -776,11 +767,8 @@ print.pai = function(x, ...) { #' @description Contains basic information about the active ingredients in the #' product #' -#' @docType class -#' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object. - ppp <- R6Class("ppp", public = list( @@ -803,12 +791,12 @@ ppp <- R6Class("ppp", 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 - #' @field density The density - #' @field density_units Defaults to g/L + #' @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") { @@ -819,13 +807,16 @@ ppp <- R6Class("ppp", self$density_units <- density_units names(self$concentrations) <- names(self$ais) self$concentration_units <- concentration_units - }, - - #' Printing method - 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: |