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This also ensures the atom bookmarks in the reactants are cleared (allows a product to be a reactant since we no longer clear the product bookmarks)
RDKit
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
- BSD license
- Core data structures and algorithms in C++
- Python (2.x and 3.x) wrapper 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
- Contrib folder with useful software harnessing the power of RDKit
Web presence
Code
Community
Materials from user group meetings
Documentation
Available on RDKit page and in Docs folder on GitHub
Installation
Installation instructions are available in Docs/Book/Install.rst.
Binary distributions, anaconda, homebrew
- Windows binaries are available with each release.
- RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
- homebrew formula for building on the Mac. Contributed by Eddie Cao.
- recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.
Projects using RDKit
- ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
- myChEMBL (blog post, paper) - A virtual machine implementation of open data and cheminformatics tools
- 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
License
Code released under the BSD license.