chents

The R package chents provides some utilities for working with chemical entities in R.

Features

• Some chemical information is retrieved from the PubChem website using the webchem package
• If Python and RDKit (> 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions some additional chemical information is computed and a 2D graph can be plotted
• Additional information can be read from a local .yaml file

Installation

You can conveniently install chents from the repository kindly made available by the R-Universe project:

install.packages("chents",
  repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org"))

In order to profit from the chemoinformatics, you need to install RDKit and its python bindings. On a Debian type Linux distribution, just use

sudo apt install python3-rdkit

If you use this package on Windows or MacOS, I would be happy to include installation instructions here if you share them with me, e.g. via a Pull Request.

Configuration of the Python version to use

On Debian type Linux distributions, you can use the following line in your global or project specific .Rprofile file to tell the reticulate package to use the system Python version that will find the RDKit installed in the system location.

Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3")

Examples

Some examples are available from the reference on jrwb.de. For example, in the example code section of the chent object docs you can see how to generate an R object for caffeine, show some of the information retrieved from PubChem and plot it by virtue of RDKit.