```{r, echo = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-" ) ``` # chents [](https://pkgdown.jrwb.de/chents/) [](https://jranke.r-universe.dev/chents) [](https://pkgdown.jrwb.de/chents/coverage/coverage.html) The R package **chents** provides some utilities for working with chemical entities in R. When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website using the [webchem](https://docs.ropensci.org/webchem/) package. ```{r} library(chents) caffeine <- chent$new("caffeine") ``` If Python and [RDKit](https://rdkit.org) (> 2015.03) are installed and configured for use with the [reticulate](https://rstudio.github.io/reticulate/) package, some additional chemical information including a 2D graph are computed. The print method gives an overview of the information that was collected. ```{r} print(caffeine) ``` There is a very simple plotting method for the chemical structure. ```{r fig.width = 2} plot(caffeine) ``` Additional information can be (but is rarely ever) read from a local .yaml file. This information can be leveraged e.g. by the [PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function of the 'pfm' package. If you have a so-called ISO common name of a pesticide active ingredient, you can use the 'pai' class derived from the 'chent' class, which starts with querying the [BCPC compendium](http://www.bcpcpesticidecompendium.org/) first. ```{r fig.width = 2} lambda <- pai$new("lambda-cyhalothrin") plot(lambda) ``` ## 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") ```