RDKit

The official sources for the RDKit library

Description

Available on the RDKit page and in the Docs folder on GitHub

Code Quality Rank: L1

Programming language: HTML

License: BSD 3-clause "New" or "Revised" License

Tags: Science And Data Analysis    

README

RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

• BSD license - a business friendly license for open source
• Core data structures and algorithms in C++
• Python 3.x wrapper generated using Boost.Python
• Java and C# wrappers generated with SWIG
• 2D and 3D molecular operations
• Descriptor and Fingerprint generation for machine learning
• Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
• Cheminformatics nodes for KNIME
• Contrib folder with useful community-contributed software harnessing the power of the RDKit

Community

• Mailing list
• GitHub discussions
• LinkedIn

Code

• GitHub code and bug tracker

Web presence

• RDKit web page
• Blog
• Documentation

Materials from user group meetings

• 2012 UGM
• 2013 UGM
• 2014 UGM
• 2015 UGM
• 2016 UGM
• 2017 UGM
• 2018 UGM
• 2019 UGM
• 2020 UGM
• 2021 UGM

Documentation

Available on the RDKit page and in the Docs folder on GitHub

Installation

Installation instructions are available in Docs/Book/Install.md.

Binary distributions, anaconda, homebrew

• binaries for conda python or, if you are using the conda-forge stack, the RDKit is also available from conda-forge.
• RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
• debs for Ubuntu and other Debian-derived Linux distros. Contributed by the Debichem team.
• homebrew formula for building on the Mac. Contributed by Eddie Cao.
• recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.
• APKs for Alpine Linux. Contributed by da Verona
• Wheels at PyPi for all major platforms and python versions. Contributed by Christopher Kuenneth

Projects using RDKit

• ChEMBL Structure Pipeline - ChEMBL protocols used to standardise and salt strip molecules.
• FPSim2 - Simple package for fast molecular similarity searches.
• Datamol (docs, repo) - A Python library to intuitively manipulate molecules.
• Scopy (docs, paper) - an integrated negative design Python library for desirable HTS/VS database design
• 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
• RDKit.js - The official JavaScript release of RDKit
• 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
• 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

License

Code released under the BSD license.