Task-Oriented Cheminformatics in R Using 'RDKit' via 'Python'.

rdkitpyr

The rdkitpyr package provides a high-level interface for cheminformatics tasks in R. It leverages the RDKit library via its Python API, accessed through the reticulate package. Unlike a thin wrapper around RDKit, rdkitpyr offers R-friendly, task-oriented functions without mirroring RDKit's native API. The package motto is "Focus on chemistry tasks in R, without diving into RDKit internals".

The name rdkitpyr (pronounced /ar-dee-kit-peer/) highlights its nested structure (from R to Python to the RDKit C++ library) and its role as an R-side peer to RDKit rather than a direct wrapper.

A key design principle is one Python call per task. Custom Python helper functions implement this approach, reducing overhead and ensuring consistent exception handling.

Installation

# Install 'rdkitpyr' from CRAN:
install.packages("rdkitpyr")

# Install 'rdkitpyr' from GitHub:
library(devtools)
install_github("andreysamokhin/rdkitpyr")

Quick Start

The rdkitpyr package supports both novice and advanced users.

• Advanced users can manually set up a Python environment (Python>=3.12, `numpy>=2,<3`, and `rdkit>=2025.9.1`) and select it in R using one of the methods recommended by reticulate (e.g., setting the RETICULATE_PYTHON_ENV environment variable or using reticulate::use_*() functions). This gives full control over package versions and the Python environment.
• Novice users do not need to install or configure Python manually. This is handled automatically by reticulate using a manifest created with reticulate::py_require(). Installation starts only when a function that requires Python is called. It may take a few minutes, and requires about 200 MB of disk space.

Here is a simple example:

library(rdkitpyr)

rdkitpyr::ConvertToInchi(c("CC", "CCC"))
#> "InChI=1S/C2H6/c1-2/h1-2H3"
#> "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"

rdkitpyr::CalculateExactMass(c("c1ccccc1", "CCCC"))
#> 78.04695 58.07825