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+# 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()
+    }
+  )
+)
+# vim: set ts=2 sw=2 expandtab: