Make the pdf structures larger, update docs

11 files changed, 23 insertions, 11 deletions

diff --git a/ChangeLog b/ChangeLog
index 9f85d81..bcdb7ba 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,19 @@
+commit 762114a5ea6393cc73a09616b937397349c1a259
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-12-05 16:00:39 +0100
+
+    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.
+
+commit 363046c178398593dea33712ba281fb5556541a6
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-10-15 01:01:21 +0200
+
+    Meta infos for pdf and self$Picture, png function
+
 commit e85f61000c139492ec6497aa3c6206a66b54d783
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2016-10-14 15:24:43 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index a753034..485797b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.2-5
-Date: 2016-12-05
+Date: 2016-12-19
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"))
 Description: Utilities for dealing with chemical entities and associated
diff --git a/R/chent.R b/R/chent.R
index b493bc2..b901904 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -181,7 +181,7 @@ chent <- R6Class("chent",
         PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw")
         PythonInR::pyImport("rdDepictor", from = "rdkit.Chem")
         PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)")
-        PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(200,250)")
+        PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)")
         PythonInR::pyExec("d2d.DrawMolecule(mol)")
         PythonInR::pyExec("d2d.FinishDrawing()")
         self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
diff --git a/man/chent.Rd b/man/chent.Rd
index 4957a89..1deb434 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -41,6 +41,7 @@ configured for use with PythonInR}
 
 \item{\code{degradation}}{List of degradation endpoints}
 }}
+
 \examples{
 oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
 print(oct)
@@ -50,4 +51,3 @@ print(caffeine)
 plot(caffeine)
 }
 \keyword{data}
-
diff --git a/man/draw_svg.chent.Rd b/man/draw_svg.chent.Rd
index c78763f..93b657d 100644
--- a/man/draw_svg.chent.Rd
+++ b/man/draw_svg.chent.Rd
@@ -21,4 +21,3 @@ draw_svg.chent(x, width = 300, height = 150,
 \description{
 Draw SVG graph from a chent object using RDKit
 }
-
diff --git a/man/pai.Rd b/man/pai.Rd
index c9d9a02..96f21d0 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -19,9 +19,9 @@ Additional chemical information is retrieved from the internet if available.
 
 \item{\code{alanwood}}{List of information retreived from www.alanwood.net/pesticides}
 }}
+
 \examples{
 atr <- pai$new("atrazine")
 print(atr)
 }
 \keyword{data}
-
diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd
index a1f618a..416675d 100644
--- a/man/plot.chent.Rd
+++ b/man/plot.chent.Rd
@@ -19,4 +19,3 @@ caffeine <- chent$new("caffeine")
 print(caffeine)
 plot(caffeine)
 }
-
diff --git a/man/pp.Rd b/man/pp.Rd
index 6adffb8..3957de7 100644
--- a/man/pp.Rd
+++ b/man/pp.Rd
@@ -22,5 +22,5 @@ An R6 class for holding information about a product with at least one active ing
 
 \item{\code{concentration_units}}{Defaults to g/L}
 }}
-\keyword{data}
 
+\keyword{data}
diff --git a/man/print.chent.Rd b/man/print.chent.Rd
index 8f9dfec..dc6a3e7 100644
--- a/man/print.chent.Rd
+++ b/man/print.chent.Rd
@@ -14,4 +14,3 @@
 \description{
 Printing method for chent objects
 }
-
diff --git a/man/print.pai.Rd b/man/print.pai.Rd
index 6206ea5..c2968b1 100644
--- a/man/print.pai.Rd
+++ b/man/print.pai.Rd
@@ -14,4 +14,3 @@
 \description{
 Printing method for pai objects (pesticidal active ingredients)
 }
-
diff --git a/test.log b/test.log
index a4eece6..abb856b 100644
--- a/test.log
+++ b/test.log
@@ -2,8 +2,8 @@ Loading chents
 Loading required package: testthat
 Testing chents
 Generation of chent objects: 
-Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
-[GCC 4.9.2]
+Initialize Python Version 3.4.2 (default, Oct  8 2014, 10:47:48) 
+[GCC 4.9.1]
 
 Trying to get chemical information from RDKit using user SMILES
 CCCCCCCCO