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-rw-r--r--R/chent.R103
1 files changed, 61 insertions, 42 deletions
diff --git a/R/chent.R b/R/chent.R
index 12ef15d..dd51798 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015 Johannes Ranke
+# Copyright (C) 2016 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package chents
@@ -19,7 +19,7 @@
#'
#' 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.
+#' python bindings are installed and configured for use with PythonInR.
#'
#' @docType class
#' @export
@@ -27,14 +27,14 @@
#' @importFrom R6 R6Class
#' @importFrom webchem get_cid cid_compinfo
#' @importFrom grImport PostScriptTrace readPicture
-#' @importFrom PythonInR pyIsConnected pyConnect pyImport pyExec pyExecg
#' @importFrom yaml yaml.load_file
#' @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 rdkit List of information obtained with RDKit, if installed and
+#' configured for use with PythonInR
#' @field Picture Graph as a \code{\link{picture}} object obtained using grImport
#' @field chyaml List of information obtained from a YAML file
#' @field degradation List of degradation endpoints
@@ -67,15 +67,17 @@ chent <- R6Class("chent",
}
if (rdkit) {
- if (is.null(self$smiles)) {
- stop("RDKit needs a SMILES code")
- } else {
- message("Trying to get chemical information from RDKit using ",
- names(self$smiles)[1], " SMILES\n",
- self$smiles[1])
- self$get_rdkit()
- self$mw <- self$rdkit$mw
- attr(self$mw, "source") <- "rdkit"
+ if(requireNamespace("PythonInR")) {
+ if (is.null(self$smiles)) {
+ stop("RDKit needs a SMILES code")
+ } else {
+ message("Trying to get chemical information from RDKit using ",
+ names(self$smiles)[1], " SMILES\n",
+ self$smiles[1])
+ self$get_rdkit()
+ self$mw <- self$rdkit$mw
+ attr(self$mw, "source") <- "rdkit"
+ }
}
}
@@ -89,19 +91,21 @@ chent <- R6Class("chent",
if (missing(identifier)) identifier <- self$identifier
pubchem_cids = webchem::get_cid(identifier)
- if (is.na(pubchem_cids[1])) {
- stop("Query ", identifier, " did not give results at PubChem")
- } else {
- message("Found ", length(pubchem_cids), " entries in PubChem, using the first one.")
- self$get_pubchem(pubchem_cids[1])
- }
+ if (is.na(pubchem_cids[1])) {
+ message("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$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid"))
+ self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]]
+
+ self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSMILES
- self$smiles["PubChem_Canonical"] <- self$pubchem$CanonicalSmiles
- if (self$pubchem$IsomericSmiles != self$pubchem$CanonicalSmiles) {
- self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSmiles
+ if (self$pubchem$IsomericSMILES != self$pubchem$CanonicalSMILES) {
+ self$smiles["PubChem_Isomeric"] <- self$pubchem$IsomericSMILES
}
self$mw = as.numeric(self$pubchem$MolecularWeight)
@@ -119,18 +123,20 @@ chent <- R6Class("chent",
}
},
get_rdkit = function() {
+ if (!requireNamespace("PythonInR"))
+ stop("PythonInR can not be loaded")
id <- names(self$identifier)
- if (!pyIsConnected()) {
- pyConnect()
+ if (!PythonInR::pyIsConnected()) {
+ PythonInR::pyConnect()
}
- try_rdkit <- try(pyImport("Chem", from = "rdkit"))
+ try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"))
if (inherits(try_rdkit, "try-error")) {
message("Could not import RDKit in Python session")
} else {
self$rdkit <- list()
- pyImport("Descriptors", from = "rdkit.Chem")
- pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')"))
- self$rdkit$mw <- pyExecg("mw = Descriptors.MolWt(mol)", "mw")
+ PythonInR::pyImport("Descriptors", from = "rdkit.Chem")
+ PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')"))
+ self$rdkit$mw <- PythonInR::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)
@@ -139,11 +145,11 @@ chent <- R6Class("chent",
}
# Create a grImport Picture
- pyImport("Draw", from = "rdkit.Chem")
+ PythonInR::pyImport("Draw", from = "rdkit.Chem")
psfile <- tempfile(fileext = ".ps")
xmlfile <- tempfile(fileext = ".xml")
cmd <- paste0("Draw.MolToFile(mol, '", psfile, "')")
- pyExec(cmd)
+ PythonInR::pyExec(cmd)
PostScriptTrace(psfile, outfilename = xmlfile)
unlink(paste0("capture", basename(psfile)))
self$Picture <- readPicture(xmlfile)
@@ -209,7 +215,8 @@ chent <- R6Class("chent",
max_occurrence = max_occurrence,
comment = comment,
source = source,
- pages = pages))
+ pages = pages,
+ stringsAsFactors = FALSE))
},
soil_degradation_endpoints = data.frame(destination = character(0),
DT50 = numeric(0),
@@ -223,6 +230,17 @@ chent <- R6Class("chent",
self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <-
c(destination, comment, pages)
self$soil_degradation_endpoints[i, "DT50"] <- DT50
+ },
+ ff = data.frame(from = character(0), to = character(0), ff = numeric(0),
+ comment = character(0), pages = character(0),
+ stringsAsFactors = FALSE),
+ add_ff = function(from = "parent", to, ff = 1, comment = "", pages = NA) {
+ i <- nrow(self$ff) + 1
+ if (from != "parent") {
+ if (!exists(from, self$TPs)) stop(from, " was not found in TPs")
+ }
+ if (!exists(to, self$TPs)) stop(to, " was not found in TPs")
+ self$ff[i, ] <- c(from, to, ff, comment, pages)
}
)
)
@@ -231,6 +249,7 @@ chent <- R6Class("chent",
#'
#' @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")
@@ -239,15 +258,14 @@ print.chent = function(x, ...) {
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$pubchem)) {
- cat ("PubChem synonyms (first 10):\n")
+ if (!is.null(x$pubchem$synonyms)) {
+ cat ("PubChem synonyms (up to 10):\n")
print(head(x$pubchem$synonyms, n = 10L))
}
}
#' Draw SVG graph from a chent object using RDKit
#'
-#' @importFrom PythonInR pyIsConnected pyConnect pyImport pyExec
#' @param x The chent object to be plotted
#' @param width The desired width in pixels
#' @param height The desired height in pixels
@@ -257,19 +275,19 @@ print.chent = function(x, ...) {
draw_svg.chent = function(x, width = 300, height = 150,
filename = paste0(names(x$identifier), ".svg"),
subdir = "svg") {
- if (!pyIsConnected()) {
- pyConnect()
+ if (!PythonInR::pyIsConnected()) {
+ PythonInR::pyConnect()
}
- try_rdkit <- try(pyImport("Chem", from = "rdkit"))
+ try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"))
if (inherits(try_rdkit, "try-error")) {
message("Could not import RDKit in Python session")
} else {
if (!dir.exists(subdir)) dir.create(subdir)
- pyExec(paste0("mol = Chem.MolFromSmiles('", x$smiles, "')"))
- pyImport("Draw", from = "rdkit.Chem")
+ PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", x$smiles, "')"))
+ PythonInR::pyImport("Draw", from = "rdkit.Chem")
cmd <- paste0("Draw.MolToFile(mol, '", file.path(subdir, filename),
"', size = (", width, ", ", height, "))")
- pyExec(cmd)
+ PythonInR::pyExec(cmd)
}
}
@@ -309,7 +327,7 @@ pai <- R6Class("pai",
if (!missing(iso) & alanwood) {
message("alanwood.net:")
- self$alanwood = webchem::alanwood(identifier, type = "commonname")
+ self$alanwood = webchem::aw_query(identifier, type = "commonname")[[1]]
if (is.na(self$alanwood[1])) {
message("Common name ", identifier, " is not known at www.alanwood.net, trying PubChem")
} else {
@@ -320,6 +338,7 @@ pai <- R6Class("pai",
attr(self$inchikey, "source") <- "alanwood"
}
}
+
super$initialize(identifier = identifier, smiles = smiles,
pubchem = pubchem, rdkit = rdkit, chyaml = chyaml)

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