Working version with basic functionality

11 files changed, 232 insertions, 24 deletions

diff --git a/ChangeLog b/ChangeLog
index 5a1734e..ee3afc4 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,4 @@
-commit 11bf23fcf72ec7c537c67786fb377635ab3d3932
+commit 7cc5df2ad1e2a1aa5c6d4d9f5865491c6b30ee2a
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2015-08-26 13:24:57 +0200
 
diff --git a/DESCRIPTION b/DESCRIPTION
index c86a2ea..4a650e0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
-Version: 0.1-1.9000
-Date: 2015-08-26
+Version: 0.1-2
+Date: 2015-09-11
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"))
 Description: Utilities for dealing with chemical entities and associated data as R objects.
diff --git a/GNUmakefile b/GNUmakefile
index 482ec37..5e8e5c1 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -30,13 +30,13 @@ clean:
 
 roxygen: 
 	@echo "Roxygenizing package..."
-	"$(R_HOME)/bin/Rscript" -e 'library(devtools); document(".")' 2>&1 | tee roxygen.log
+	"$(R_HOME)/bin/Rscript" -e 'library(devtools); document(".")'
 	@echo "DONE."
 
 $(TGZ): $(pkgfiles)
 	sed -i -e "s/Date:.*/Date: $(DATE)/" DESCRIPTION
 	@echo "Roxygenizing package..."
-	"$(R_HOME)/bin/Rscript" -e 'library(devtools); document(".")' 2>&1 | tee roxygen.log
+	"$(R_HOME)/bin/Rscript" -e 'library(devtools); document(".")'
 	@echo "Building package..."
 	git log --no-merges -M --date=iso > ChangeLog
 	"$(R_HOME)/bin/R" CMD build .
diff --git a/NAMESPACE b/NAMESPACE
index 4cdb514..e96d4f7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,10 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
+S3method(print,chent)
+S3method(print,pai)
 export(chent)
 export(pai)
+export(pp)
 importFrom(R6,R6Class)
 importFrom(webchem,cid_compinfo)
 importFrom(webchem,get_cid)
diff --git a/R/chent.R b/R/chent.R
index 90e3baf..1ef26be 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -30,6 +30,7 @@
 #' @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
 #' @example inst/examples/chents.R
 #' @keywords data
 
@@ -40,20 +41,31 @@ chent <- R6Class("chent",
     smiles = NULL,
     mw = NULL,
     pubchem = NULL,
-    initialize = function(identifier, type = c("name", "smiles"), 
-                          source = c("pubchem")) {
+    rdkit = NULL,
+    initialize = function(identifier, smiles = NULL,
+                          source = c("rdkit", "pubchem")) {
       self$identifier <- identifier
-      type = match.arg(type)
-      attr(self$identifier, "type") <- type
-      source = match.arg(source)      
+      names(self$identifier) <- make.names(identifier)
+      source = match.arg(source)
       switch(source,
         pubchem = {
           self$try_pubchem(identifier)
+        },
+        rdkit = {
+          if (is.null(smiles)) {
+            stop("rdkit needs smiles as input")
+          } else {
+            self$smiles <- smiles
+            self$get_rdkit()
+            self$mw <- self$rdkit$mw
+            attr(self$mw, "source") <- "rdkit"
+          }
         }
       )
       invisible(self)
     },
     try_pubchem = function(identifier) {
+      if (missing(identifier)) identifier <- self$identifier
       pubchem_cids = webchem::get_cid(identifier)
 
         if (is.na(pubchem_cids[1])) {
@@ -83,19 +95,94 @@ chent <- R6Class("chent",
         }
       }
     },
-    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$synonyms, n = 10L))
+    get_rdkit = function() {
+      if (require(PythonInR)) {
+        id <- names(self$identifier)
+        try_rdkit <- try(pyImport("Chem", from = "rdkit"))
+        if (inherits(try_rdkit, "try-error")) {
+          message("Could not import RDKit in Python session")
+        } else {
+          self$rdkit <- list()
+          pyImport("Descriptors", from = "rdkit.Chem")
+          pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles, "')"))
+          self$rdkit$mw <- pyExecg("mw = Descriptors.MolWt(mol)", "mw")
+          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$mw)
+            }
+          }
+        }
+      } else {
+        stop("rdkit not available as PythonInR is not installed")
+      }
+    },
+    TPs = list(),
+    add_TP = function(x, smiles = NULL) {
+      if (inherits(x, "chent")) {
+        id <- names(x$identifier)
+        chent <- x
+      } else {
+        id <- make.names(x)
+        chent <- chent$new(x, smiles) 
       }
+      self$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, 
+                                  comment = "", 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, 
+                                               comment = comment, 
+                                               source = source,
+                                               pages = pages))
+    },
+    soil_degradation_endpoints = data.frame(destination = character(0), 
+                                            DT50 = numeric(0),
+                                            comment = character(0),
+                                            pages = character(0),
+                                            stringsAsFactors = FALSE),
+    add_soil_degradation_endpoints = function(destination, DT50 = NA,
+                                              comment = "", pages = NA) {
+      i <- nrow(self$soil_degradation_endpoints) + 1
+      self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- 
+        c(destination, comment, pages)
+      self$soil_degradation_endpoints[i, "DT50"] <- DT50
     }
   )
 )
 
+#' Printing method for chent objects
+#'
+#' @param x The chent object to be printed
+#' @param ... Further arguments for compatibility with the S3 method
+#' @export
+print.chent = function(x, ...) {
+  cat("<chent>\n")
+  cat("Identifier $identifier", x$identifier, "\n")
+  cat ("InChI Key $inchikey", x$inchikey, "\n")
+  cat ("SMILES string $smiles", x$smiles, "\n")
+  if (!is.null(x$mw)) cat ("Molecular weight $mw:", round(x$mw, 1), "\n")
+  if (!is.null(x$pubchem)) {
+    cat ("PubChem synonyms (first 10):\n")
+    print(head(x$pubchem$synonyms, n = 10L))
+  }
+}
+
 #' An R6 class for pesticidal active ingredients and associated data
 #' 
 #' The class is initialised with an identifier which is generally an ISO common name.
@@ -118,6 +205,7 @@ pai <- R6Class("pai",
     initialize = function(identifier, type = c("name", "smiles"), 
                           source = c("alanwood", "pubchem")) {
       self$identifier <- identifier
+      names(self$identifier) <- make.names(identifier)
       type = match.arg(type)
       attr(self$identifier, "type") <- type
       source = match.arg(source)      
@@ -137,17 +225,71 @@ pai <- R6Class("pai",
             # Get additional information from PubChem
             pubchem_cids = get_cid(identifier)
             self$get_pubchem(pubchem_cids[[1]])
+            self$get_rdkit()
           }
         },
         pubchem = {
           self$try_pubchem(identifier)
+          self$get_rdkit()
         }
       )
       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("<pai> with ISO common name $iso", self$iso, "\n")
-      super$show()
+      cat("<pp> named", self$name, "\n")
     }
   )
 )
diff --git a/inst/examples/chents.R b/inst/examples/chents.R
index 7fb3286..0309e2b 100644
--- a/inst/examples/chents.R
+++ b/inst/examples/chents.R
@@ -1,2 +1,3 @@
-oct <- chent$new("1-octanol")
+oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
+oct$try_pubchem()
 print(oct)
diff --git a/man/chent.Rd b/man/chent.Rd
index ed304f5..c42863d 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -24,9 +24,12 @@ from the internet.
 \item{\code{mw}}{Molecular weight, with attribute 'source'}
 
 \item{\code{pubchem}}{List of information retreived from PubChem}
+
+\item{\code{rdkit}}{List of information obtained with RDKit}
 }}
 \examples{
-oct <- chent$new("1-octanol")
+oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
+oct$try_pubchem()
 print(oct)
 }
 \keyword{data}
diff --git a/man/pp.Rd b/man/pp.Rd
new file mode 100644
index 0000000..5be85bf
--- /dev/null
+++ b/man/pp.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/chent.R
+\docType{class}
+\name{pp}
+\alias{pp}
+\title{R6 class for holding a product with at least one active ingredient}
+\format{An \code{\link{R6Class}} generator object.}
+\usage{
+pp
+}
+\description{
+An R6 class for holding information about a product with at least one active ingredient
+}
+\section{Fields}{
+
+\describe{
+\item{\code{name}}{The name of the product}
+
+\item{\code{ais}}{A list of active ingredients}
+
+\item{\code{concentrations}}{The concentration of the ais}
+
+\item{\code{concentration_units}}{Defaults to g/L}
+}}
+\keyword{data}
+
diff --git a/man/print.chent.Rd b/man/print.chent.Rd
new file mode 100644
index 0000000..56f04f5
--- /dev/null
+++ b/man/print.chent.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/chent.R
+\name{print.chent}
+\alias{print.chent}
+\title{Printing method for chent objects}
+\usage{
+\method{print}{chent}(x, ...)
+}
+\arguments{
+\item{x}{The chent object to be printed}
+
+\item{...}{Further arguments for compatibility with the S3 method}
+}
+\description{
+Printing method for chent objects
+}
+
diff --git a/man/print.pai.Rd b/man/print.pai.Rd
new file mode 100644
index 0000000..d7ee332
--- /dev/null
+++ b/man/print.pai.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/chent.R
+\name{print.pai}
+\alias{print.pai}
+\title{Printing method for pai objects (pesticidal active ingredients)}
+\usage{
+\method{print}{pai}(x, ...)
+}
+\arguments{
+\item{x}{The chent object to be printed}
+
+\item{...}{Further arguments for compatibility with the S3 method}
+}
+\description{
+Printing method for pai objects (pesticidal active ingredients)
+}
+
diff --git a/roxygen.log b/roxygen.log
index f691b87..0205542 100644
--- a/roxygen.log
+++ b/roxygen.log
@@ -1,4 +1,3 @@
 Updating chents documentation
 Loading chents
-Writing chent.Rd
-Writing pai.Rd
+Writing print.pai.Rd