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4f2ec84e7b
* update .gitignore * foundation for 3D descriptors move PBF into core * cleanup work * a bit more cleanup * move the principal moments calc to MolTransforms * cleanup * cleanups * add caching of the principal moments and values * do not include the 3D descriptors in MolDescriptors.h * the properties are computed * add PMI descriptors and tests * add tests for NPR descriptors * return 0 when the largest PMI is zero * PMI edge case tests * NPR edge case tests * PBF edge case tests * PBF edge case tests * more edge cases * add a few more 3d descriptors * add defns to docs * tests for the new descriptors * add versions to new descriptors * add 3d descriptors to python wrapper * add eigen support to the travis build * try to get non-windows builds working * remove computeCovarianceMatrix() from java wrapper * make pmi property names "private"
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 (2.x and 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
Web presence
- RDKit web page
- Blog
- Documentation also available at ReadTheDocs
Code
Community
Materials from user group meetings
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
- 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
- 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
License
Code released under the BSD license.