Read, preprocess, and featurize chemical data using RDKit.
The tidychem
package offers a lightweight R interface for accessing RDKit via the RDKit Python API.
First of all, install RDKit. Make sure it is discoverable by reticulate.
Then install tidychem
with:
remotes::install_github("nanxstats/tidychem")
reticulate::use_python("/usr/local/bin/python3")
library("tidychem")
"smi-multiple.smi" %>%
tidychem_example() %>%
read_smiles() %>%
fp_morgan()
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.
tidychem is free and open source software, licensed under GPL-3.