From 6248971edad72b30f7f609a6bb2217d0b41498a0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2016 22:08:48 +0100 Subject: Make the pdf structures larger, update docs --- ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 2 +- R/chent.R | 2 +- man/chent.Rd | 2 +- man/draw_svg.chent.Rd | 1 - man/pai.Rd | 2 +- man/plot.chent.Rd | 1 - man/pp.Rd | 2 +- man/print.chent.Rd | 1 - man/print.pai.Rd | 1 - test.log | 4 ++-- 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 +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 +Date: 2016-10-15 01:01:21 +0200 + + Meta infos for pdf and self$Picture, png function + commit e85f61000c139492ec6497aa3c6206a66b54d783 Author: Johannes Ranke Date: 2016-10-14 15:24:43 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index a753034..485797b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: chents Type: Package Title: Chemical Entities as R Objects Version: 0.2-5 -Date: 2016-12-05 +Date: 2016-12-19 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de")) Description: Utilities for dealing with chemical entities and associated diff --git a/R/chent.R b/R/chent.R index b493bc2..b901904 100644 --- a/R/chent.R +++ b/R/chent.R @@ -181,7 +181,7 @@ chent <- R6Class("chent", PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw") PythonInR::pyImport("rdDepictor", from = "rdkit.Chem") PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)") - PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(200,250)") + PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)") PythonInR::pyExec("d2d.DrawMolecule(mol)") PythonInR::pyExec("d2d.FinishDrawing()") self$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 -- cgit v1.2.1