Use new rdkit drawing code

This is SVG only, therefore use grConvert to convert
to postscript before importing using grImport.
SVG size is currently hardcoded.

3 files changed, 28 insertions, 11 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index c50c9b4..a753034 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,18 +2,19 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.2-5
-Date: 2016-10-14
+Date: 2016-12-05
 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. If Python and RDKit are installed and configured for use
-    with 'PythonInR', some basic chemoinformatics functions like the calculation
-    of molecular weight and plotting of chemical structures in R graphics are
-    available.
+    data as R objects. If Python and RDKit (> 2015.03) are installed and
+    configured for use with 'PythonInR', some basic chemoinformatics functions
+    like the calculation of molecular weight and plotting of chemical
+    structures in R graphics are available.
 Imports:
     webchem,
     R6,
     grImport,
+    grConvert,
     yaml
 Suggests:
     knitr,
@@ -25,4 +26,4 @@ LazyData: yes
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: http://cgit.jrwb.de/chents
-RoxygenNote: 5.0.1
+RoxygenNote: 5.0.1.9000
diff --git a/R/chent.R b/R/chent.R
index bbb46b3..b493bc2 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -35,6 +35,7 @@
 #' @field pubchem List of information retreived from PubChem
 #' @field rdkit List of information obtained with RDKit, if installed and
 #'   configured for use with PythonInR
+#' @field svg SVG code
 #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport
 #' @field Pict_font_size Font size as extracted from the intermediate PostScript file
 #' @field pdf_height Height of the MediaBox in the pdf after cropping
@@ -52,6 +53,7 @@ chent <- R6Class("chent",
     mw = NULL,
     pubchem = NULL,
     rdkit = NULL,
+    svg = NULL,
     Picture = NULL,
     Pict_font_size = NULL,
     pdf_height = NULL,
@@ -174,19 +176,31 @@ chent <- R6Class("chent",
           }
         }
 
-        # Create a grImport Picture 
+        # 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)")
+        PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(200,250)")
+        PythonInR::pyExec("d2d.DrawMolecule(mol)")
+        PythonInR::pyExec("d2d.FinishDrawing()")
+        self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
+        svgfile <- tempfile(fileext = ".svg")
+        writeLines(self$svg, svgfile)
+
+        # Convert to PostScript, remembering size properties
         psfile <- tempfile(fileext = ".ps")
-        xmlfile <- tempfile(fileext = ".xml")
-        cmd <- paste0("Draw.MolToFile(mol, '", psfile, "')")
-        PythonInR::pyExec(cmd)
+        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"), 
diff --git a/man/chent.Rd b/man/chent.Rd
index 62d6e01..4957a89 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -29,6 +29,8 @@ python bindings are installed and configured for use with PythonInR.
 \item{\code{rdkit}}{List of information obtained with RDKit, if installed and
 configured for use with PythonInR}
 
+\item{\code{svg}}{SVG code}
+
 \item{\code{Picture}}{Graph as a \code{\link{picture}} object obtained using grImport}
 
 \item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file}