# 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
#'
#' 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 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$new("1-octanol", smiles = "CCCCCCCCO")
#' print(oct)
#' if (!is.null(oct$Picture)) {
#' plot(oct)
#' }
#'
#' caffeine <- chent$new("caffeine")
#' print(caffeine)
#' if (!is.null(caffeine$Picture)) {
#' plot(caffeine)
#' }
chent <- R6Class("chent",
public <- list(
identifier = NULL,
inchikey = NULL,
smiles = NULL,
mw = NULL,
pubchem = NULL,
rdkit = NULL,
mol = NULL,
svg = NULL,
Picture = NULL,
Pict_font_size = NULL,
pdf_height = NULL,
p0 = NULL,
cwsat = NULL,
PUF = NULL,
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) {
self$identifier <- identifier
names(self$identifier) <- make.names(identifier)
pubchem_from = match.arg(pubchem_from)
self$smiles <- c(user = smiles)
if (pubchem) {
if (pubchem_from == 'name') {
query = identifier
} else {
query = get(pubchem_from)
}
self$try_pubchem(query, from = pubchem_from)
}
if (rdkit) {
if(rdkit_available) {
if (is.null(self$smiles)) {
message("RDKit would need a SMILES code")
} else {
message("Trying to get chemical information from RDKit using ",
names(self$smiles)[1], " SMILES\n",
self$smiles[1])
self$get_rdkit(template = template)
self$mw <- self$rdkit$mw
attr(self$mw, "source") <- "rdkit"
}
} else {
message("RDKit is not available")
}
}
if (chyaml) {
self$get_chyaml()
}
invisible(self)
},
try_pubchem = function(query, from = 'name') {
message("PubChem:")
if (missing(query)) query <- self$identifier
pubchem_result = webchem::get_cid(query, from = from, match = "first")
if (is.na(pubchem_result[[1, "cid"]])) {
message("Query ", query, " did not give results at PubChem")
} else {
self$get_pubchem(pubchem_result[[1, "cid"]])
}
},
get_pubchem = function(pubchem_cid) {
self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid",
properties = c("MolecularFormula", "MolecularWeight",
"CanonicalSMILES", "IsomericSMILES",
"InChI", "InChIKey", "IUPACName",
"XLogP", "TPSA", "Complexity", "Charge",
"HBondDonorCount", "HBondAcceptorCount")))
self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]]
self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSMILES
if (self$pubchem$IsomericSMILES != self$pubchem$CanonicalSMILES) {
self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSMILES
}
self$mw = as.numeric(self$pubchem$MolecularWeight)
attr(self$mw, "source") <- "pubchem"
if (is.null(self$inchikey)) {
self$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")
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$inchikey, "source"))
} else {
attr(self$inchikey, "source") <- c(attr(self$inchikey, "source"), "pubchem")
}
}
}
},
get_rdkit = function(template = NULL) {
if(!rdkit_available) {
stop("RDKit is not available")
}
self$rdkit <- list()
self$mol <- rdkit_module$Chem$MolFromSmiles(self$smiles[1])
self$rdkit$mw <- rdkit_module$Chem$Descriptors$MolWt(self$mol)
if (!is.null(self$mw)) {
if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {
message("RDKit mw is ", self$rdkit$mw)
message("mw is ", self$mw)
}
}
# Create an SVG representation
rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol)
if (!is.null(template)) {
rdkit_template <- rdkit_module$Chem$MolFromSmiles(template)
rdkit_module$Chem$rdDepictor$Compute2DCoords(template)
rdkit$Chem$AllChem$GenerateDepictionMatching2DStructure(self$mol, template)
}
d2d <- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L)
d2d$DrawMolecule(self$mol)
d2d$FinishDrawing()
self$svg <- d2d$GetDrawingText()
svgfile <- tempfile(fileext = ".svg")
psfile <- tempfile(fileext = ".ps")
writeLines(self$svg, svgfile)
rsvg::rsvg_ps(svgfile, psfile)
# Get size properties useful for plotting
ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
ps_font_size <- gsub(" .*$", "", ps_font_line)
self$Pict_font_size = as.numeric(ps_font_size)
# Read in to create Picture
xmlfile <- tempfile(fileext = ".xml")
PostScriptTrace(psfile, outfilename = xmlfile)
unlink(paste0("capture", basename(psfile)))
self$Picture <- readPicture(xmlfile)
unlink(c(xmlfile, psfile, svgfile))
},
get_chyaml = function(repo = c("wd", "local", "web"),
chyaml = paste0(URLencode(self$identifier), ".yaml")) {
repo = match.arg(repo)
paths = c(wd = ".",
local = file.path("~", "git/chyaml"))
chyaml_handlers = list(
expr = function(x) NULL, # To avoid security risks from reading chyaml files
dataframe = function(x)
eval(parse(text = paste0("data.frame(", x, ", stringsAsFactors = FALSE)"))))
if (repo %in% c("wd", "local")) {
path = paths[repo]
full = file.path(path, chyaml)
if (!file.exists(full)) {
message("Did not find chyaml file ", full)
} else {
if (is(try(self$chyaml <- yaml.load_file(chyaml, handlers = chyaml_handlers)),
"try-error")) {
message("Could not load ", full)
} else {
message("Loaded ", full)
}
}
} else {
message("web repositories not implemented")
}
},
add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {
self$p0 <- p0
attr(self$p0, "T") <- T
attr(self$p0, "source") <- source
attr(self$p0, "page") <- page
attr(self$p0, "remark") <- remark
},
add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") {
self$cwsat <- cwsat
attr(self$cwsat, "T") <- T
attr(self$cwsat, "pH") <- pH
attr(self$cwsat, "source") <- source
attr(self$cwsat, "page") <- page
attr(self$cwsat, "remark") <- remark
},
add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") {
self$PUF <- PUF
attr(self$PUF, "source") <- source
attr(self$PUF, "page") <- page
attr(self$PUF, "remark") <- remark
},
TPs = list(),
add_TP = function(x, smiles = NULL, pubchem = FALSE) {
if (inherits(x, "chent")) {
id <- names(x$identifier)
chent <- x
} else {
id <- make.names(x)
chent <- chent$new(x, smiles, pubchem = pubchem)
}
self$TPs[[id]] <- chent
},
transformations = data.frame(study_type = character(0),
TP_identifier = character(0),
max_occurrence = numeric(0),
source = character(0),
pages = character(0),
stringsAsFactors = FALSE),
add_transformation = function(study_type, TP_identifier, max_occurrence,
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()"))
}
TP_chent <- self$TPs[TP_name]
if (is.numeric(pages)) pages <- paste(pages, collapse = ", ")
cn <- colnames(self$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))
},
soil_degradation = NULL,
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) {
new_soil_degradation = data.frame(
soil = soils,
DT50_mod = DT50_mod,
DT50_mod_ref = DT50_mod_ref,
type = type,
country = country,
pH_orig = pH_orig,
pH_medium = pH_medium,
pH_H2O = pH_H2O,
perc_OC = perc_OC,
temperature = temperature,
moisture = moisture,
category = category,
formulation = formulation,
model = model,
chi2 = chi2,
remark = remark,
source = source,
page = page,
stringsAsFactors = FALSE)
if (is.null(self$soil_degradation)) {
self$soil_degradation <- new_soil_degradation
} else {
self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation)
}
},
soil_ff = NULL,
add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) {
new_soil_ff = data.frame(
target = target,
soil = soils,
ff = ff,
remark = remark,
source = source,
page = page,
stringsAsFactors = FALSE)
if (is.null(self$soil_ff)) {
self$soil_ff <- new_soil_ff
} else {
self$soil_ff <- rbind(self$soil_ff, new_soil_ff)
}
},
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) {
new_soil_sorption = data.frame(
soils = soils,
Kf = Kf, Kfoc = Kfoc, N = N,
type = type,
pH_orig = pH_orig,
pH_medium = pH_medium,
pH_H2O = pH_H2O,
perc_OC = perc_OC, perc_clay = perc_clay, CEC = CEC,
remark = remark,
source = source,
page = page,
stringsAsFactors = FALSE)
if (is.null(self$soil_sorption)) {
self$soil_sorption <- new_soil_sorption
} else {
self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption)
}
},
pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf",
template = NULL) {
if (!dir.exists(dir)) {
message("Directory '", dir, "' does not exist")
message("Trying to create directory '", dir, "'")
dir.create(dir, recursive = TRUE)
}
path = file.path(dir, file)
message("Creating file '", path, "'")
pdf(path)
plot(self)
dev.off()
message("Cropping file '", path, "' using pdfcrop")
bash_path <- shQuote(path)
system(paste("pdfcrop --margin 10", bash_path, bash_path, "> /dev/null"))
# Get the height of the MediaBox
head <- readLines(path, n = 20, skipNul = TRUE)
m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE))
self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line))
},
png = function(file = paste0(self$identifier, ".png"), dir = "structures/png",
antialias = 'gray') {
if (!dir.exists(dir)) {
message("Directory '", dir, "' does not exist")
message("Trying to create directory '", dir, "'")
dir.create(dir, recursive = TRUE)
}
path = file.path(dir, file)
message("Creating file '", path, "'")
png(path, antialias = antialias)
plot(self)
dev.off()
},
emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") {
if (!requireNamespace("devEMF")) {
stop("You need to have the devEMF package installed for this function")
}
if (!dir.exists(dir)) {
message("Directory '", dir, "' does not exist")
message("Trying to create directory '", dir, "'")
dir.create(dir, recursive = TRUE)
}
path = file.path(dir, file)
message("Creating file '", path, "'")
devEMF::emf(path)
plot(self)
dev.off()
}
)
)
#' Printing method for chent objects
#'
#' @param x The chent object to be printed
#' @param ... Further arguments for compatibility with the S3 method
#' @importFrom utils head
#' @export
print.chent = function(x, ...) {
cat("<chent>\n")
cat("Identifier $identifier", x$identifier, "\n")
cat ("InChI Key $inchikey", x$inchikey, "\n")
cat ("SMILES string $smiles:\n")
print(x$smiles)
if (!is.null(x$mw)) cat ("Molecular weight $mw:", round(x$mw, 1), "\n")
if (!is.null(x$pubchem$synonyms)) {
cat ("PubChem synonyms (up to 10):\n")
print(head(x$pubchem$synonyms, n = 10L))
}
}
#' Draw SVG graph from a chent object using RDKit
#'
#' @param x The chent object to be plotted
#' @param width The desired width in pixels
#' @param height The desired height in pixels
#' @param filename The filename
#' @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$identifier), ".svg"),
subdir = "svg") {
if (!rdkit_available) {
stop("RDkit is not available via reticulate")
} else {
if (!dir.exists(subdir)) dir.create(subdir)
mol <- rdkit_module$Chem$MolFromSmiles(x$smiles)
rdkit_module$Chem$Draw$MolToFile(mol, file.path(subdir, filename),
size = c(as.integer(width), as.integer(height)))
}
}
#' Plot method for chent objects
#'
#' @importFrom grImport grid.picture
#' @param x The chent object to be plotted
#' @param ... Further arguments passed to \code{\link{grid.picture}}
#' @export
#' @examples
#' caffeine <- chent$new("caffeine")
#' print(caffeine)
#' if (!is.null(caffeine$Picture)) {
#' plot(caffeine)
#' }
plot.chent = function(x, ...) {
if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?")
grid.picture(x$Picture)
}
#' An R6 class for pesticidal active ingredients and associated data
#'
#' The class is initialised with an identifier which is generally an ISO common name.
#' Additional chemical information is retrieved from the internet if available.
#'
#' @docType class
#' @importFrom R6 R6Class
#' @export
#' @format An \code{\link{R6Class}} generator object
#' @field iso ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org
#' @field bcpc List of information retrieved from pesticidecompendium.bcpc.org
#' @keywords data
#' @examples
#' # On Travis, we get a certificate validation error,
#' # likely because the system (xenial) is so old,
#' # therefore don't run this example on Travis
#' if (Sys.getenv("TRAVIS") == "") {
#'
#' atr <- pai$new("atrazine")
#' print(atr)
#' if (!is.null(atr$Picture)) {
#' plot(atr)
#' }
#'
#' }
pai <- R6Class("pai",
inherit = chent,
public <- list(
iso = NULL,
bcpc = NULL,
initialize = function(iso, identifier = iso,
smiles = NULL, smiles_source = 'user',
inchikey = NULL, inchikey_source = 'user',
bcpc = TRUE,
pubchem = TRUE, pubchem_from = 'auto',
rdkit = TRUE, template = NULL,
chyaml = TRUE)
{
if (!is.null(inchikey)) {
self$inchikey = inchikey
attr(self$inchikey, "source") <- "user"
}
if (!missing(iso) & bcpc) {
message("BCPC:")
bcpc_result = webchem::bcpc_query(identifier, from = "name")
# Use first element of list, as we passed a query of length one
if (is.na(bcpc_result[[1]][1])) {
message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem")
} else {
self$bcpc = bcpc_result[[1]]
self$iso = self$bcpc$cname
attr(self$iso, "source") <- "bcpc"
attr(self$iso, "status") <- self$bcpc$status
bcpc_ik = self$bcpc$inchikey
if (length(bcpc_ik) == 1 && nchar(bcpc_ik) == 27 && !is.na(bcpc_ik)) {
if (is.null(self$inchikey)) {
self$inchikey = self$bcpc$inchikey
attr(self$inchikey, "source") <- "bcpc"
} else {
if (bcpc_ik == self$inchikey) {
attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc")
} else {
warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org")
}
}
}
}
}
# Set pubchem_from if not specified
if (pubchem_from == 'auto') {
pubchem_from = 'name'
if (!is.null(self$inchikey)) {
pubchem_from = 'inchikey'
}
}
super$initialize(identifier = identifier,
smiles = smiles, smiles_source = smiles_source,
inchikey = self$inchikey,
pubchem = pubchem, pubchem_from = pubchem_from,
rdkit = rdkit, template = template, chyaml = chyaml)
invisible(self)
}
)
)
#' Printing method for pai objects (pesticidal active ingredients)
#'
#' @param x The chent object to be printed
#' @param ... Further arguments for compatibility with the S3 method
#' @export
print.pai = function(x, ...) {
cat("<pai> with ISO common name $iso", x$iso, "\n")
print.chent(x)
if (length(x$TPs) > 0) {
cat("\nTransformation products:\n")
print(x$TPs)
}
if (nrow(x$transformations) > 0) {
cat("\nTransformations:\n")
print(x$transformations)
}
}
#' R6 class for holding a product with at least one active ingredient
#'
#' An R6 class for holding information about a product with at least one active ingredient
#'
#' @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(
name = NULL,
ais = list(),
concentrations = NULL,
concentration_units = NULL,
density = NULL,
density_units = "g/L",
initialize = function(name, ..., concentrations, concentration_units = "g/L",
density = 1000, density_units = "g/L") {
self$name <- name
self$ais <- list(...)
self$concentrations <- concentrations
self$density <- density
self$density_units <- density_units
names(self$concentrations) <- names(self$ais)
self$concentration_units <- concentration_units
},
print = function() {
cat("<pp> named", self$name, "\n")
}
)
)
# vim: set ts=2 sw=2 expandtab:
