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RDKit Docker Image

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

This Docker image provides a Debian distribution with Python 3 and all other dependencies installed via the Debian package manager. RDKit is compiled from source.

This Docker image is designed to provide a lightweight RDKit installation, without any unnecessary build tools or package management infrastructure in the final image. Other images may inherit from it, or use it as an earlier stage in a multi-stage build process. See the mcs07/postgres-rdkit image for an example of this.

For a more complete environment that is easier to work with but results in a larger image, you may be better served by using a miniconda image and using conda install to add RDKit and other dependencies.


Run rdkit container with an interactive shell:

docker run -it --rm mcs07/rdkit:latest /bin/bash

Or a python interpreter:

docker run -it --rm mcs07/rdkit:latest python3


A multi-stage docker build is used to produce a lightweight production image without all the build dependencies. To build, run:

docker build -t rdkit .

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