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3f3ff3858a
* refactor skeleton * fix contribs * adapt documentation * clarify function names * make variable names more readable and update documentation * switch boost dynamic bitset with std::vector<bool> * clearer const name * fix typo and go back to dynamic bitset * go back to old function signature * add inline overload with fewer arguments * remove unecessary doc lines and add tol to distance directly in function call * use constexpr for known distance force constant * update documentation * enhance documentation * english Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * make changes requested by @greglandrum * make all constexprs --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
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
Code
Web presence
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
- 2022 UGM
- 2023 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
- ROBERT - Automated Machine Learning Protocols
- AQME - Automated Quantum Mechanical Environment
- chemprop - message passing neural networks for molecular property prediction
- RMG - Reaction Mechanism Generator
- RDMC - Reaction Data and Molecular Conformers - package for dealing with reactions, molecules, conformers, mainly in 3D
- pychemprojections - python library for visualizing various 2D projections of molecules.
- pychemovality - python library for estimating the ovality of molecules.
- 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.