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¶
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This will, inevitably, be out of date.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
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
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.”