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 website using the webchem package.
library(chents)
caffeine <- chent$new("caffeine")
#> Querying PubChem ...
#> Trying to get chemical information from RDKit using PubChem SMILES
#> CN1C=NC2=C1C(=O)N(C(=O)N2C)CIf Python and RDKit (> 2015.03) are installed and configured for use with the reticulate package, some additional chemical information including a 2D graph are computed.
The print method gives an overview of the information that was collected.
print(caffeine)
#> <chent>
#> Identifier $identifier caffeine
#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#> SMILES string $smiles:
#> PubChem
#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#> Molecular weight $mw: 194.2
#> PubChem synonyms (up to 10):
#> [1] "caffeine" "58-08-2"
#> [3] "Guaranine" "1,3,7-Trimethylxanthine"
#> [5] "Methyltheobromine" "Theine"
#> [7] "Thein" "Cafeina"
#> [9] "Koffein" "Mateina"There is a very simple plotting method for the chemical structure.
plot(caffeine)
Additional information can be (but is rarely ever) read from a local .yaml file. This information can be leveraged e.g. by the PEC_soil function of the ‘pfm’ package.
If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the BCPC compendium first.
lambda <- pai$new("lambda-cyhalothrin")
#> Querying BCPC for lambda-cyhalothrin ...
#> Querying PubChem ...
#> Trying to get chemical information from RDKit using PubChem SMILES
#> CC1([C@@H]([C@@H]1C(=O)O[C@@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)/C=C(/C(F)(F)F)\Cl)C
#> RDKit mw is 449.856
#> mw is 449.8
plot(lambda)
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.
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")