# 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
- 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
- Releases every 6 months
- Web presence:
  - Homepage: http://www.rdkit.org Documentation, links
  - Github (https://github.com/rdkit) Downloads, bug tracker, git repository
  - Sourceforge (http://sourceforge.net/projects/rdkit) Mailing lists
  - Blog (https://rdkit.blogspot.com) Tips, tricks, random stuff
  - Tutorials (https://github.com/rdkit/rdkit-tutorials) Jupyter-based tutorials for using the RDKit
  - 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:
  - Twitter: @RDKit_org
  - LinkedIn: https://www.linkedin.com/groups/8192558
  - Slack: https://rdkit.slack.com (invite required, contact Greg)

### History:

- 2000-2006: Developed and used at Rational Discovery for building predictive models for ADME, Tox, biological activity
- June 2006: Open-source (BSD license) release of software, Rational Discovery shuts down
- to present: Open-source development continues, use within Novartis, contributions from Novartis back to open-source version

## 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

## Usage by other open-source projects

This will, inevitably, be out of date. If you know of others, please let us know or submit a pull request!

- stk (docs, paper) - a Python library for building, manipulating, analyzing and automatic design of molecules.
- gpusimilarity - A Cuda/Thrust implementation of fingerprint similarity searching
- Samson Connect - Software for adaptive modeling and simulation of nanosystems
- mol_frame - Chemical Structure Handling for Dask and Pandas DataFrames
- RDKitjs - port of RDKit functionality to JavaScript
- DeepChem - python library for deep learning for chemistry
- mmpdb - Matched molecular pair database generation and analysis
- CheTo (paper)- Chemical topic modeling
- OCEAN (paper)- Optimized cross reactivity estimation
- ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
- myChEMBL (blog post, paper) - A virtual machine implementation of open data and cheminformatics tools
- ZINC - Free database of commercially-available compounds for virtual screening
- sdf_viewer.py - an interactive SDF viewer
- sdf2ppt - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
- MolGears - A cheminformatics tool for bioactive molecules
- PYPL - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
- shape-it-rdkit - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
- WONKA - Tool for analysis and interrogation of protein-ligand crystal structures
- OOMMPPAA - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
- OCEAN - web-tool for target-prediction of chemical structures which uses ChEMBL as datasource
- chemfp - very fast fingerprint searching
- rdkit_ipynb_tools - RDKit Tools for the IPython Notebook
- Vernalis KNIME nodes
- Erlwood KNIME nodes
- AZOrange

## The Contrib Directory

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

## Footnotes

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

## License

This document is copyright (C) 2013-2018 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.”