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authorJohannes Ranke <jranke@uni-bremen.de>2019-02-19 18:17:38 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-02-19 18:19:37 +0100
commit132bd73395033a95163080517b5a7c371cf512a2 (patch)
tree46f69d36bf47c1906f2b8876371121142d9984dd /R
parentaa80ce4f46f9ff1a2851ba9ba873a55a8f6ebc6d (diff)
Fix check for rdkit availability
Also remove python-rdkit from the travis config as its version is too old on travis (Ubuntu trusty)
Diffstat (limited to 'R')
-rw-r--r--R/chent.R122
1 files changed, 68 insertions, 54 deletions
diff --git a/R/chent.R b/R/chent.R
index 941b430..6a5abc7 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2016,2017,2018 Johannes Ranke
+# Copyright (C) 2016-2019 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package chents
@@ -88,7 +88,7 @@ chent <- R6Class("chent",
}
if (rdkit) {
- if(requireNamespace("PythonInR", quietly = TRUE)) {
+ if(rdkit_available()) {
if (is.null(self$smiles)) {
message("RDKit would need a SMILES code")
} else {
@@ -99,6 +99,8 @@ chent <- R6Class("chent",
self$mw <- self$rdkit$mw
attr(self$mw, "source") <- "rdkit"
}
+ } else {
+ message("RDKit is not available via PythonInR")
}
}
@@ -162,62 +164,54 @@ chent <- R6Class("chent",
}
},
get_rdkit = function(template = NULL) {
- if (!requireNamespace("PythonInR"))
- stop("PythonInR can not be loaded")
- id <- names(self$identifier)
- if (!PythonInR::pyIsConnected()) {
- PythonInR::pyConnect()
+ if(!rdkit_available()) {
+ stop("RDKit is not available via PythonInR")
}
- try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"))
- if (inherits(try_rdkit, "try-error")) {
- message("Could not import RDKit in Python session")
- } else {
- self$rdkit <- list()
- PythonInR::pyImport("Descriptors", from = "rdkit.Chem")
- PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$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)
- message("mw is ", self$mw)
- }
+ self$rdkit <- list()
+ 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$mw)
+ message("mw is ", self$mw)
}
+ }
- # Create an SVG representation
- PythonInR::pyImport("Draw", from = "rdkit.Chem")
- PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw")
- PythonInR::pyImport("rdDepictor", from = "rdkit.Chem")
- PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)")
- if (!is.null(template)) {
- PythonInR::pyImport("AllChem", from = "rdkit.Chem")
- PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')"))
- PythonInR::pyExec("AllChem.Compute2DCoords(template)")
- PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)")
- }
- PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)")
- PythonInR::pyExec("d2d.DrawMolecule(mol)")
- PythonInR::pyExec("d2d.FinishDrawing()")
- self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
+ # Create an SVG representation
+ PythonInR::pyImport("Draw", from = "rdkit.Chem")
+ PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw")
+ PythonInR::pyImport("rdDepictor", from = "rdkit.Chem")
+ PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)")
+ if (!is.null(template)) {
+ PythonInR::pyImport("AllChem", from = "rdkit.Chem")
+ PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')"))
+ PythonInR::pyExec("AllChem.Compute2DCoords(template)")
+ PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)")
+ }
+ PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)")
+ PythonInR::pyExec("d2d.DrawMolecule(mol)")
+ PythonInR::pyExec("d2d.FinishDrawing()")
+ self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
- if (!requireNamespace("grConvert")) {
- stop("grConvert is not available, self$Picture will not be created")
- } else {
- # Convert to PostScript, remembering size properties
- svgfile <- tempfile(fileext = ".svg")
- writeLines(self$svg, svgfile)
- psfile <- tempfile(fileext = ".ps")
- suppressMessages(grConvert::convertPicture(svgfile, psfile))
- ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
- ps_font_size <- gsub(" .*$", "", ps_font_line)
- self$Pict_font_size = as.numeric(ps_font_size)
-
- # Read in to create Picture
- xmlfile <- tempfile(fileext = ".xml")
- PostScriptTrace(psfile, outfilename = xmlfile)
- unlink(paste0("capture", basename(psfile)))
- self$Picture <- readPicture(xmlfile)
- unlink(c(xmlfile, psfile, svgfile))
- }
+ if (!requireNamespace("grConvert")) {
+ stop("grConvert is not available, self$Picture will not be created")
+ } else {
+ # Convert to PostScript, remembering size properties
+ svgfile <- tempfile(fileext = ".svg")
+ writeLines(self$svg, svgfile)
+ psfile <- tempfile(fileext = ".ps")
+ suppressMessages(grConvert::convertPicture(svgfile, psfile))
+ ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
+ ps_font_size <- gsub(" .*$", "", ps_font_line)
+ self$Pict_font_size = as.numeric(ps_font_size)
+
+ # Read in to create Picture
+ xmlfile <- tempfile(fileext = ".xml")
+ PostScriptTrace(psfile, outfilename = xmlfile)
+ unlink(paste0("capture", basename(psfile)))
+ self$Picture <- readPicture(xmlfile)
+ unlink(c(xmlfile, psfile, svgfile))
}
},
get_chyaml = function(repo = c("wd", "local", "web"),
@@ -607,4 +601,24 @@ pp <- R6Class("pp",
}
)
)
+
+rdkit_available <- function()
+{
+ if(requireNamespace("PythonInR", quietly = TRUE)) {
+ if (!PythonInR::pyIsConnected()) {
+ PythonInR::pyConnect()
+ }
+ sink(tempfile())
+ try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"),
+ silent = TRUE)
+ sink()
+ if (inherits(try_rdkit, "try-error")) {
+ return(FALSE)
+ } else {
+ return(TRUE)
+ }
+ } else {
+ return(FALSE)
+ }
+}
# vim: set ts=2 sw=2 expandtab:

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