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-rw-r--r--R/chent.R399
1 files changed, 286 insertions, 113 deletions
diff --git a/R/chent.R b/R/chent.R
index c89efec..6d18277 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -1,54 +1,19 @@
-# 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
#' @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)
@@ -61,27 +26,78 @@
#' }
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.
+ #'
+ #' @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$identifier) <- make.names(identifier)
@@ -120,6 +136,10 @@ chent <- R6Class("chent",
}
invisible(self)
},
+
+ #' Try to get chemical information from PubChem
+ #' @param query Query string to be passed to [get_cid][webchem::get_cid]
+ #' @param from Passed to [get_cid][webchem::get_cid]
try_pubchem = function(query, from = 'name') {
message("PubChem:")
if (missing(query)) query <- self$identifier
@@ -131,6 +151,9 @@ 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 +193,9 @@ 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 +238,19 @@ chent <- R6Class("chent",
self$Picture <- readPicture(xmlfile)
unlink(c(xmlfile, psfile, svgfile))
},
+
+ #' Obtain information from a YAML file
+ #' @param repo Should the file be looked for in the current working
+ #' directory, a local git repository under `~/git/chyaml`, or from
+ #' the web (not implemented).
+ #' @param chyaml The filename to be looked for
get_chyaml = function(repo = c("wd", "local", "web"),
- chyaml = paste0(URLencode(self$identifier), ".yaml")) {
+ chyaml = paste0(URLencode(self$identifier), ".yaml"))
+ {
repo = match.arg(repo)
- paths = c(wd = ".",
- local = file.path("~", "git/chyaml"))
+ paths = c(
+ wd = ".",
+ local = file.path("~", "git/chyaml"))
chyaml_handlers = list(
expr = function(x) NULL, # To avoid security risks from reading chyaml files
@@ -240,6 +274,13 @@ chent <- R6Class("chent",
message("web repositories not implemented")
}
},
+
+ #' Add a vapour pressure
+ #' @param p0 The vapour pressure in Pa
+ #' @param T Temperature
+ #' @param source An acronym specifying the source of the information
+ #' @param page The page from which the information was taken
+ #' @param remark A remark
add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {
self$p0 <- p0
attr(self$p0, "T") <- T
@@ -247,7 +288,17 @@ chent <- R6Class("chent",
attr(self$p0, "page") <- page
attr(self$p0, "remark") <- remark
},
- add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") {
+
+ #' Add a water solubility
+ #' @param cwsat The water solubility in mg/L
+ #' @param T Temperature
+ #' @param pH The pH value
+ #' @param source An acronym specifying the source of the information
+ #' @param page The page from which the information was taken
+ #' @param remark A remark
+ add_cwsat = function(cwsat, T = NA, pH = NA,
+ source = NA, page = NA, remark = "")
+ {
self$cwsat <- cwsat
attr(self$cwsat, "T") <- T
attr(self$cwsat, "pH") <- pH
@@ -255,13 +306,29 @@ 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") {
+
+ #' 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")
+ {
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$identifier)
@@ -272,14 +339,28 @@ chent <- R6Class("chent",
}
self$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),
+ TP_identifier = character(0),
+ max_occurrence = numeric(0),
+ 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$TPs`
+ #' @param max_occurrence The maximum observed occurrence of the
+ #' transformation product, expressed as a fraction of the amount that would
+ #' result from stochiometric transformation
+ #' @param source An acronym specifying the source of the information
+ #' @param pages The page from which the information was taken
+ #' @param remark A remark
add_transformation = function(study_type, TP_identifier, max_occurrence,
- remark = "", source = NA, pages = NA) {
+ remark = "", source = NA, pages = NA)
+ {
TP_name = make.names(TP_identifier)
if (!inherits(self$TPs[[TP_name]], "chent")) {
stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()"))
@@ -288,23 +369,49 @@ chent <- R6Class("chent",
if (is.numeric(pages)) pages <- paste(pages, collapse = ", ")
cn <- colnames(self$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,
+
+ #' 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')
+ #' @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
+ #' @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,
- 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 +438,20 @@ 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) {
+
+ # 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 +464,23 @@ 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)
+ #' 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) {
+ 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 +499,13 @@ chent <- R6Class("chent",
self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption)
}
},
- pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf",
- template = NULL) {
+
+ #' Write a PDF image of the structure
+ #' @param file The file to write to
+ #' @param dir The directory to write the file to
+ #' @param template A template expressed as SMILES to use in RDKit
+ pdf = function(file = paste0(self$identifier, ".pdf"),
+ dir = "structures/pdf", template = NULL) {
if (!dir.exists(dir)) {
message("Directory '", dir, "' does not exist")
message("Trying to create directory '", dir, "'")
@@ -393,8 +525,12 @@ 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') {
+
+ #' Write a PNG image of the structure
+ #' @param antialias Passed to [png][grDevices::png]
+ png = function(file = paste0(self$identifier, ".png"),
+ dir = "structures/png", antialias = 'gray')
+ {
if (!dir.exists(dir)) {
message("Directory '", dir, "' does not exist")
message("Trying to create directory '", dir, "'")
@@ -406,7 +542,12 @@ chent <- R6Class("chent",
plot(self)
dev.off()
},
- emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") {
+
+ #' Write an EMF image of the structure using [emf][devEMF::emf]
+ #' @param file The file to write to
+ emf = function(file = paste0(self$identifier, ".emf"),
+ dir = "structures/emf")
+ {
if (!requireNamespace("devEMF")) {
stop("You need to have the devEMF package installed for this function")
}
@@ -452,8 +593,8 @@ print.chent = function(x, ...) {
#' @param subdir The path to which the file should be written
#' @export
draw_svg.chent = function(x, width = 300, height = 150,
- filename = paste0(names(x$identifier), ".svg"),
- subdir = "svg") {
+ filename = paste0(names(x$identifier), ".svg"),
+ subdir = "svg") {
if (!rdkit_available) {
stop("RDkit is not available via reticulate")
} else {
@@ -482,18 +623,16 @@ plot.chent = function(x, ...) {
grid.picture(x$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 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,
@@ -510,16 +649,32 @@ 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,
+
+ #' 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
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 = TRUE)
{
if (!is.null(inchikey)) {
@@ -564,10 +719,9 @@ 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$inchikey,
+ pubchem = pubchem, pubchem_from = pubchem_from,
+ rdkit = rdkit, template = template, chyaml = chyaml)
invisible(self)
}
@@ -592,30 +746,47 @@ print.pai = function(x, ...) {
}
}
-#' R6 class for holding a product with at least one active ingredient
+#' @title R6 class for a plant protection product with at least one active ingredient
#'
-#' An R6 class for holding information about a product with at least one active ingredient
+#' @description Contains basic information about the active ingredients in the
+#' product
#'
#' @docType class
#' @importFrom R6 R6Class
#' @export
#' @format An \code{\link{R6Class}} generator object.
-#' @field name The name of the product
-#' @field ais A list of active ingredients
-#' @field concentrations The concentration of the ais
-#' @field concentration_units Defaults to g/L
-#' @keywords data
-
-pp <- R6Class("pp",
- public <- list(
+
+ppp <- R6Class("ppp",
+ public = list(
+
+ #' @field name The name of the product
name = NULL,
+
+ #' @field ais A list of active ingredients
ais = list(),
+
+ #' @field concentrations The concentration of the ais
concentrations = NULL,
+
+ #' @field concentration_units Defaults to g/L
concentration_units = NULL,
+
+ #' @field density The density of the product
density = NULL,
+
+ #' @field density_units Defaults to g/L
density_units = "g/L",
+
+ #' Creates a new instance of this [R6][R6::R6Class] class.
+ #'
+ #' @field ... Identifiers of the active ingredients
+ #' @field concentrations Concentrations of the active ingredients
+ #' @field concentration_units Defaults to g/L
+ #' @field density The density
+ #' @field density_units Defaults to g/L
initialize = function(name, ..., concentrations, concentration_units = "g/L",
- density = 1000, density_units = "g/L") {
+ density = 1000, density_units = "g/L")
+ {
self$name <- name
self$ais <- list(...)
self$concentrations <- concentrations
@@ -624,6 +795,8 @@ pp <- R6Class("pp",
names(self$concentrations) <- names(self$ais)
self$concentration_units <- concentration_units
},
+
+ #' Printing method
print = function() {
cat("<pp> named", self$name, "\n")
}

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