An overview of the RDKit

What is it?

Open source toolkit for cheminformatics

• Business-friendly BSD license

• Core data structures and algorithms in C++

• Python 3.x wrappers generated using Boost.Python

• Java and C# wrappers generated with SWIG

• JavaScript wrappers of most-important functionality

• 2D and 3D molecular operations

• Descriptor generation for machine learning

• Molecular database cartridge for PostgreSQL

• Cheminformatics nodes for KNIME (distributed from the KNIME community site: https://www.knime.com/rdkit)

Operational:

• http://www.rdkit.org

• Supports Mac/Windows/Linux

• Major releases every 6 months, minor release about once a month

• Web presence:

  • Homepage: https://www.rdkit.org Documentation, links

  • Github (https://github.com/rdkit) Downloads, discussion, bug tracker, git repository

  • Sourceforge (https://sourceforge.net/projects/rdkit) Mailing lists

  • Blog (https://greglandrum.github.io/rdkit-blog/) Tips, tricks, random stuff

  • KNIME integration (https://github.com/rdkit/knime-rdkit) RDKit nodes for KNIME

• Mailing lists at https://sourceforge.net/p/rdkit/mailman/, searchable archives available for rdkit-discuss and rdkit-devel

• Social media:

  • BlueSky: @rdkit.bsky.social

  • Mastodon: rdkit@mastodon.social

  • LinkedIn: https://www.linkedin.com/groups/8192558

  • Slack: https://rdkit.slack.com (invite required, contact Greg)

Citing the RDKit

There is no official RDKit publication, our recommended citation is:

RDKit: Open-source cheminformatics. https://www.rdkit.org

We also recommend that you include the DOI for the version of the RDKit you used in the work. You can look these up here: https://doi.org/10.5281/zenodo.591637

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Integration with other open-source projects

• KNIME: Workflow and analytics tool

• PostgreSQL: Extensible relational database

• Django: “The web framework for perfectionists with deadlines”

• SQLite: “The most used database engine in the world”

• Lucene: Text-search engine [1]

The Contrib Directory

The Contrib directory, part of the standard RDKit distribution, includes code that has been contributed by members of the community.

License

This document is copyright (C) 2013-2024 by Greg Landrum

This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.

The intent of this license is similar to that of the RDKit itself. In simple words: “Do whatever you want with it, but please give us some credit.”

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[1]

These implementations are functional but are not necessarily the best, fastest, or most complete.