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* Adds C++ Enumeration Engine to the RDKit * Adds Sanitization helpers, wrappers and tests * Clang format * Remove unused enumerationStateOnly flag * Fixes docStrings to current API * Adds doc strings * Removes RGroupPosition, adds getPosition to EnumerationBase * Fixes readability. * Adds EnumerateLibraryBase::reset and getReaction * Added getReagents method to EnumerateLibrary * Make the tests have the same naming * Need to save the initial state for resetting. * Stupid case-insensitive file systems * Moves ResetState to EnumerateLibraryBase * Adds removeNonmatchingReagents helper * Renames currentPosition to getPosition * Adds Enumeration Toolkit tutorial * Fixes Python3 serialization and enumerators * Verified to run on python2 and 3 * Fixes integer issues on windows * The number of enumeration should be unsigned. * Adds deserialization constructor * Moves boost_serialization to the end * Deprecates Clone in favor of copy * Update tests to use copy.copy not Clone * Move RGROUPS and BBS into an EnumerationTypes namespace * Make sure old pickles work * Adds pickle for backwards compatibility * Moves to uint64_t from size_t for public api * Whups, accidentally used the binary archiver. * Commits boost 1.55 serialization * Makes serialization turnoffable Like Filter Catalog * Fixes tests when serialization not available. Adds more enumeration strategy tests * Fixes a syntax error on some versions of python * Fixes sanitizeRxn to actually make proper RGroup atoms * Updates SanitizeRXN python API * Updates Enumeration API to a parameter class - fixes reagent removal * Adds a mess of tests * Change stats to return a string. * Exposes EvenPairSamplingStrategy Stats to python * Fixes a crash bug in SanitizeRxn * Adds better testing of the even pair sampling * Fixes namespace * One more try to fix gcc * Enum classes are c++11 and a microsoft extension. * Fix typo * Fixes np.median for python3 * Fixes atom iterators * Adds virtual tags to derived virtual functions (for clarity) * Fixes size comparison issues * Adds doc string * Small cleanup (has no effect since flags aren’t used) * fixes crash bug on windows * get the tests working on windows * Updates tutorial * Adds Glare implementation to Contrib
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.