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diff --git a/README.rmd b/README.rmd new file mode 100644 index 0000000..4fe26ea --- /dev/null +++ b/README.rmd @@ -0,0 +1,91 @@ +<!-- README.md is generated from README.rmd. Please edit that file --> + +```{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") +``` + |