# 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This will, inevitably, be out of date.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!

- Datamol (docs, repo) - A Python library to intuitively manipulate molecules.

- DockOnSurf (docs, paper) - A high-throughput python code to automatically find the most stable geometry for molecules adsorbed on surfaces.

- Scopy (docs, paper) - an integrated negative design Python library for desirable HTS/VS database design

- Open Force Field Toolkit - A parametrization engine for force fields based on direct chemical perception.

- 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.”