# 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:

### 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](https://www.knime.com/rdkit): Workflow and analytics tool - [PostgreSQL](https://github.com/rdkit/rdkit/blob/master/Docs/Book/Cartridge.rst): Extensible relational database - [Django](http://django-rdkit.readthedocs.org/en/latest/): “The web framework for perfectionists with deadlines” - [SQLite](https://github.com/rvianello/chemicalite): “The most used database engine in the world” - [Lucene](https://github.com/rdkit/org.rdkit.lucene): Text-search engine [1](#footnote1)

## Usage by other open-source projects This will, inevitably, be out of date.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!

a Python library for building, manipulating, analyzing and automatic design of molecules. - [gpusimilarity](https://github.com/schrodinger/gpusimilarity) - A Cuda/Thrust implementation of fingerprint similarity searching - [Samson Connect](https://www.samson-connect.net) - Software for adaptive modeling and simulation of nanosystems - [mol_frame](https://github.com/apahl/mol_frame) - Chemical Structure Handling for Dask and Pandas DataFrames - [RDKitjs](https://github.com/cheminfo/RDKitjs) - port of RDKit functionality to JavaScript - [DeepChem](https://deepchem.io) - python library for deep learning for chemistry - [mmpdb](https://github.com/rdkit/mmpdb) - Matched molecular pair database generation and analysis - [CheTo](https://github.com/rdkit/CheTo) ([paper](http://pubs.acs.org/doi/10.1021/acs.jcim.7b00249))- Chemical topic modeling - [OCEAN](https://github.com/rdkit/OCEAN) ([paper](http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00067))- Optimized cross reactivity estimation - [ChEMBL Beaker](https://github.com/mnowotka/chembl_beaker) - standalone web server wrapper for RDKit and OSRA - [myChEMBL](https://github.com/chembl/mychembl) ([blog post](http://chembl.blogspot.de/2013/10/chembl-virtual-machine-aka-mychembl.html), [paper](http://bioinformatics.oxfordjournals.org/content/early/2013/11/20/bioinformatics.btt666)) - A virtual machine implementation of open data and cheminformatics tools - [ZINC](http://zinc15.docking.org) - Free database of commercially-available compounds for virtual screening - [sdf_viewer.py](https://github.com/apahl/sdf_viewer) - an interactive SDF viewer - [sdf2ppt](https://github.com/dkuhn/sdf2ppt) - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation. - [MolGears](https://github.com/admed/molgears) - A cheminformatics tool for bioactive molecules - [PYPL](http://www.biochemfusion.com/downloads/#OracleUtilities) - Simple cartridge that lets you call Python scripts from Oracle PL/SQL. - [shape-it-rdkit](https://github.com/jandom/shape-it-rdkit) - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend - [WONKA](http://wonka.sgc.ox.ac.uk/WONKA/) - Tool for analysis and interrogation of protein-ligand crystal structures - [OOMMPPAA](http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/) - Tool for directed synthesis and data analysis based on protein-ligand crystal structures - [OCEAN](https://github.com/rdkit/OCEAN) - web-tool for target-prediction of chemical structures which uses ChEMBL as datasource - [chemfp](http://chemfp.com) - very fast fingerprint searching - [rdkit_ipynb_tools](https://github.com/apahl/rdkit_ipynb_tools) - RDKit Tools for the IPython Notebook - [Vernalis KNIME nodes](https://www.knime.com/book/vernalis-nodes-for-knime-trusted-extension) - [Erlwood KNIME nodes](https://www.knime.com/community/erlwood) - [AZOrange](https://github.com/AZcompTox/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

<a name=”footnote1”>1</a>: 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.”