From f908377f1de2e04ca3720d10084169c46a477ce2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 28 Sep 2015 21:34:23 +0200
Subject: Several changes heading for a release to the public

- Add tests
- Add staticdocs
- Documentation improvements
- Several small code improvements
---
 man/chent.Rd          | 12 ++++++++++--
 man/draw_svg.chent.Rd | 24 ++++++++++++++++++++++++
 man/plot.chent.Rd     | 23 +++++++++++++++++++++++
 3 files changed, 57 insertions(+), 2 deletions(-)
 create mode 100644 man/draw_svg.chent.Rd
 create mode 100644 man/plot.chent.Rd

(limited to 'man')

diff --git a/man/chent.Rd b/man/chent.Rd
index c42863d..da68b56 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -9,8 +9,9 @@
 chent
 }
 \description{
-The class is initialised with an identifier. Chemical information is retrieved
-from the internet.
+The class is initialised with an identifier. Chemical information is retrieved from
+the internet. Additionally, it can be generated using RDKit if RDKit and its
+python bindings are installed.
 }
 \section{Fields}{
 
@@ -26,11 +27,18 @@ from the internet.
 \item{\code{pubchem}}{List of information retreived from PubChem}
 
 \item{\code{rdkit}}{List of information obtained with RDKit}
+
+\item{\code{Picture}}{Graph as a \code{\link{picture}} object obtained using grImport}
 }}
 \examples{
 oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
 oct$try_pubchem()
 print(oct)
+plot(oct)
+caffeine <- chent$new("caffeine", source = "pubchem")
+print(caffeine)
+caffeine$get_rdkit()
+plot(caffeine)
 }
 \keyword{data}
 
diff --git a/man/draw_svg.chent.Rd b/man/draw_svg.chent.Rd
new file mode 100644
index 0000000..87234a1
--- /dev/null
+++ b/man/draw_svg.chent.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/chent.R
+\name{draw_svg.chent}
+\alias{draw_svg.chent}
+\title{Draw SVG graph from a chent object using RDKit}
+\usage{
+draw_svg.chent(x, width = 300, height = 150,
+  filename = paste0(names(x$identifier), ".svg"), subdir = "svg")
+}
+\arguments{
+\item{x}{The chent object to be plotted}
+
+\item{width}{The desired width in pixels}
+
+\item{height}{The desired height in pixels}
+
+\item{filename}{The filename}
+
+\item{subdir}{The path to which the file should be written}
+}
+\description{
+Draw SVG graph from a chent object using RDKit
+}
+
diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd
new file mode 100644
index 0000000..f2e7572
--- /dev/null
+++ b/man/plot.chent.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/chent.R
+\name{plot.chent}
+\alias{plot.chent}
+\title{Plot method for chent objects}
+\usage{
+\method{plot}{chent}(x, ...)
+}
+\arguments{
+\item{x}{The chent object to be plotted}
+
+\item{...}{Further arguments passed to \code{\link{grid.picture}}}
+}
+\description{
+Plot method for chent objects
+}
+\examples{
+caffeine <- chent$new("caffeine", source = "pubchem")
+print(caffeine)
+caffeine$get_rdkit()
+plot(caffeine)
+}
+
-- 
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