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-rw-r--r--R/chent.R103
1 files changed, 79 insertions, 24 deletions
diff --git a/R/chent.R b/R/chent.R
index fe87d5e..6606992 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -53,23 +53,31 @@ chent <- R6Class("chent",
Picture = NULL,
chyaml = NULL,
degradation = NULL,
- initialize = function(identifier, smiles = NULL,
- rdkit = TRUE, pubchem = TRUE,
+ initialize = function(identifier, smiles = NULL, smiles_source = 'user',
+ inchikey = NULL, inchikey_source = 'user',
+ pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'),
+ rdkit = TRUE,
chyaml = TRUE) {
self$identifier <- identifier
names(self$identifier) <- make.names(identifier)
+ pubchem_from = match.arg(pubchem_from)
self$smiles <- c(user = smiles)
if (pubchem) {
- self$try_pubchem(identifier)
+ if (pubchem_from == 'name') {
+ query = identifier
+ } else {
+ query = get(pubchem_from)
+ }
+ self$try_pubchem(query, from = pubchem_from)
}
if (rdkit) {
if(requireNamespace("PythonInR", quietly = TRUE)) {
if (is.null(self$smiles)) {
- stop("RDKit needs a SMILES code")
+ message("RDKit would need a SMILES code")
} else {
message("Trying to get chemical information from RDKit using ",
names(self$smiles)[1], " SMILES\n",
@@ -86,16 +94,19 @@ chent <- R6Class("chent",
}
invisible(self)
},
- try_pubchem = function(identifier) {
+ try_pubchem = function(query, from = 'name') {
message("PubChem:")
- if (missing(identifier)) identifier <- self$identifier
- pubchem_cids = webchem::get_cid(identifier)[[identifier]]
+ if (missing(query)) query <- self$identifier
+ pubchem_result = webchem::get_cid(query, from = from)
- if (is.na(pubchem_cids[1])) {
- message("Query ", identifier, " did not give results at PubChem")
+ if (is.na(pubchem_result[[1]][1])) {
+ message("Query ", query, " did not give results at PubChem")
} else {
- message("Found ", length(pubchem_cids), " entries in PubChem, using the first one.")
- self$get_pubchem(pubchem_cids[1])
+ n_results = length(pubchem_result[[1]])
+ if (n_results > 1) {
+ warning("Found ", n_results, " entries in PubChem, using the first one.")
+ }
+ self$get_pubchem(pubchem_result[[1]][1])
}
},
get_pubchem = function(pubchem_cid) {
@@ -115,10 +126,20 @@ chent <- R6Class("chent",
self$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"))
+ 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")
+ }
}
}
},
@@ -319,7 +340,7 @@ plot.chent = function(x, ...) {
#' 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.
+#' Additional chemical information is retrieved from the internet if available.
#'
#' @docType class
#' @importFrom R6 R6Class
@@ -335,26 +356,60 @@ pai <- R6Class("pai",
public <- list(
iso = NULL,
alanwood = NULL,
- initialize = function(iso, identifier = iso, smiles = NULL, alanwood = TRUE,
- pubchem = TRUE, rdkit = TRUE, chyaml = TRUE) {
+ initialize = function(iso, identifier = iso,
+ smiles = NULL, smiles_source = 'user',
+ inchikey = NULL, inchikey_source = 'user',
+ alanwood = TRUE,
+ pubchem = TRUE, pubchem_from = 'auto',
+ rdkit = TRUE, chyaml = TRUE)
+ {
+ if (!is.null(inchikey)) {
+ self$inchikey = inchikey
+ attr(self$inchikey, "source") <- "user"
+ }
if (!missing(iso) & alanwood) {
message("alanwood.net:")
- self$alanwood = webchem::aw_query(identifier, type = "commonname")[[1]]
- if (is.na(self$alanwood[1])) {
+ aw_result = webchem::aw_query(identifier, type = "commonname")
+
+ # Use first element of list, as we passed a query of length one
+ if (is.na(aw_result[[1]][1])) {
message("Common name ", identifier, " is not known at www.alanwood.net, trying PubChem")
} else {
+ self$alanwood = aw_result[[1]]
self$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"
+ aw_ik = self$alanwood$inchikey
+ if (length(aw_ik) == 1 && nchar(aw_ik) == 27 && !is.na(aw_ik)) {
+ if (is.null(self$inchikey)) {
+ self$inchikey = self$alanwood$inchikey
+ attr(self$inchikey, "source") <- "alanwood"
+ } else {
+ if (aw_ik == self$inchikey) {
+ attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "alanwood")
+ } else {
+ warning("InChIKey ", self$inchikey, " differs from ", aw_ik, " obtained from alanwood.net")
+ }
+ }
+ }
+ }
+ }
+
+ # Set pubchem_from if not specified
+ if (pubchem_from == 'auto') {
+ pubchem_from = 'name'
+ if (!is.null(self$inchikey)) {
+ pubchem_from = 'inchikey'
}
}
- super$initialize(identifier = identifier, smiles = smiles,
- pubchem = pubchem, rdkit = rdkit, chyaml = chyaml)
+ super$initialize(identifier = identifier,
+ smiles = smiles, smiles_source = smiles_source,
+ inchikey = self$inchikey,
+ pubchem = pubchem, pubchem_from = pubchem_from,
+ rdkit = rdkit, chyaml = chyaml)
invisible(self)
}

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