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tidychem

Lifecycle: experimental R-CMD-check

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.

License

tidychem is free and open source software, licensed under GPL-3.