# Copyright (C) 2015 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.
#'
#' @docType class
#' @export
#' @format An \code{\link{R6Class}} generator object
#' @importFrom R6 R6Class
#' @importFrom webchem get_cid cid_compinfo
#' @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
#' @example inst/examples/chents.R
#' @keywords data
chent <- R6Class("chent",
public <- list(
identifier = NULL,
inchikey = NULL,
smiles = NULL,
mw = NULL,
pubchem = NULL,
initialize = function(identifier, type = c("name", "smiles"),
source = c("pubchem")) {
self$identifier <- identifier
type = match.arg(type)
attr(self$identifier, "type") <- type
source = match.arg(source)
switch(source,
pubchem = {
self$try_pubchem(identifier)
}
)
invisible(self)
},
try_pubchem = function(identifier) {
pubchem_cids = webchem::get_cid(identifier)
if (is.na(pubchem_cids[1])) {
stop("Query ", identifier, " did not give results at PubChem")
} else {
message("Found ", length(pubchem_cids), " entries in PubChem, using the first one.")
self$get_pubchem(pubchem_cids[1])
}
},
get_pubchem = function(pubchem_cid) {
self$pubchem = webchem::cid_compinfo(pubchem_cid)
self$smiles = self$pubchem$CanonicalSmiles
attr(self$smiles, "source") <- "pubchem"
attr(self$smiles, "type") <- "canonical"
self$mw = as.numeric(self$pubchem$MolecularWeight)
attr(self$mw, "source") <- "pubchem"
if (is.null(self$inchikey)) {
self$inchikey <- self$pubchem$InChIKey
attr(self$inchikey, "source") <- "pubchem"
} else {
if (self$pubchem$InChIKey != self$inchikey) {
stop("InChiKey of PubChem record does not the one retreived from ",
attr(self$inchi, "source"))
}
}
},
show = function() {
cat("<chent> built using $identifier", self$identifier, "\n")
cat ("InChI Key $inchikey", self$inchikey, "\n")
cat ("SMILES string $smiles", self$smiles, "\n")
if (!is.null(self$mw)) cat ("Molecular weight $mw:", round(self$mw, 1), "\n")
if (!is.null(self$pubchem)) {
cat ("PubChem synonyms (first 10):\n")
print(head(self$pubchem$synonyms, n = 10L))
}
}
)
)
#' An R6 class for pesticidal active ingredients and associated data
#'
#' The class is initialised with an identifier which is generally an ISO common name.
#' Additional chemical information is retrieved from the internet.
#'
#' @docType class
#' @importFrom R6 R6Class
#' @export
#' @format An \code{\link{R6Class}} generator object
#' @field iso ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides
#' @field alanwood List of information retreived from www.alanwood.net/pesticides
#' @example inst/examples/ai.R
#' @keywords data
pai <- R6Class("pai",
inherit = chent,
public <- list(
iso = NULL,
alanwood = NULL,
initialize = function(identifier, type = c("name", "smiles"),
source = c("alanwood", "pubchem")) {
self$identifier <- identifier
type = match.arg(type)
attr(self$identifier, "type") <- type
source = match.arg(source)
switch(source,
alanwood = {
self$alanwood = webchem::alanwood(identifier, type = "commonname")
if (is.na(self$alanwood[1])) {
message("Common name ", identifier, " is not known at www.alanwood.net, trying PubChem")
self$try_pubchem(identifier)
} else {
self$iso = self$alanwood$cname
attr(self$iso, "source") <- "alanwood"
attr(self$iso, "status") <- self$alanwood$status
self$inchikey = self$alanwood$inchikey
attr(self$inchikey, "source") <- "alanwood"
# Get additional information from PubChem
pubchem_cids = get_cid(identifier)
self$get_pubchem(pubchem_cids[[1]])
}
},
pubchem = {
self$try_pubchem(identifier)
}
)
invisible(self)
},
print = function() {
cat("<pai> with ISO common name $iso", self$iso, "\n")
super$show()
}
)
)
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