Read, preprocess, and featurize chemical data using RDKit.
The tidychem package offers a lightweight R interface for accessing RDKit via the RDKit Python API.
Installation
First of all, install RDKit. Make sure it is discoverable by reticulate.
Then install tidychem with:
remotes::install_github("nanxstats/tidychem")Usage
reticulate::use_python("/usr/local/bin/python3")
library("tidychem")
"smi-multiple.smi" %>%
tidychem_example() %>%
read_smiles() %>%
fp_morgan()Developers
If you have already installed Python and tidychem, and want to develop tidychem in RStudio, simply create a file .Rprofile under the package directory and set the Python binary path (Homebrew Python 3 path example below):
Sys.setenv(RETICULATE_PYTHON = "/usr/local/bin/python3")The next time you open the project, the correct Python path and library path should be already set. For more technical details, see reticulate Python version configuration.