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authorJohannes Ranke <jranke@uni-bremen.de>2016-12-19 22:08:48 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-12-19 22:08:48 +0100
commit6248971edad72b30f7f609a6bb2217d0b41498a0 (patch)
tree9ae320df20beb648abe0621d6e56d856676bab13
parent762114a5ea6393cc73a09616b937397349c1a259 (diff)
Make the pdf structures larger, update docs
-rw-r--r--ChangeLog16
-rw-r--r--DESCRIPTION2
-rw-r--r--R/chent.R2
-rw-r--r--man/chent.Rd2
-rw-r--r--man/draw_svg.chent.Rd1
-rw-r--r--man/pai.Rd2
-rw-r--r--man/plot.chent.Rd1
-rw-r--r--man/pp.Rd2
-rw-r--r--man/print.chent.Rd1
-rw-r--r--man/print.pai.Rd1
-rw-r--r--test.log4
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

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