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* First import of GaussianShape. * Tidying. * Custom features. * Optimise. * Optimise. * Return 3 scores rather than 2 including combo score. * Rename useFeatures to useColors. * Python wrappers. * Python tests. * Take out big test. * Add new start mode, as PubChem does it. * Doh! * Fix MolTransforms eigenvalue return. * Two cycle optimisation, mostly working. * Take out bestSoFar score from SCA. * Take out DTYPE. * Tidy out redundant variables. * Optimisation in 2 parts. * More fiddling in pursuit of speed. * Update Python wrapper. * Tweak. * Atom subsets and different radii. * Fix test. * Revert pubchem_shape's test.cpp. * Serialize ShapeInput. * Trigger build * Remove pointers to std::arrays in ShapeInput. * ShapeInput virtual d'tor. * Precondition - ShapeInput needs a molecule with at least 1 conformer. * Rename ShapeInput::d_centroid to ShapeInput::d_canonTrans. * Fix normalization bugs. * Select start mode using moments of inertia rather than eigenvalues of canonical transformation. * Include color features in moments of inertia. * Smidge faster. * Tversky similarity. * Tidy tests. * Tests working on Linux. * Revert force of right handed axes in MolTransforms::computePrincipalAxesAndMomentsFromGyrationMatrix replacing with a comment in the code. * Response to review. * Sneaky allCarbon bug. * add multithreaded test * Response to review. * Doh! Don't recalculate normalization after every transformation. * Re-instate d_normalizationOK. * Re-name functions for fetching canonical transformations. * Separate alpha from coords. * MultiConf works with single conf extraction. * Extract all conformations. Max and best similarities. * Renames d_currConformer to d_activeShape. * Update shapeToMol. * Update shapeToMol. * Changes from synthon shape searching. * Fix normalization of multiple confs. * Update Python wrappers. * Fix shape merge. * Improve bestSimilarity. * Fix python wrapper. * Pull in changes from SynthonShapeSearch: make pruneShapes public. function to negate Alpha values. * clang-tidy suggestions. * clang-tidy suggestions. * Bug in quaternion gradients - we now have only 3 coordinates. * Tidy tests. * Mac result slightly different. * Multi conformer molecule alignment. * Optionally return raw overlap volumes in score functions. * Python wrappers for raw overlap volumes. * Update Python wrapper ShapeInputOptions. * Tidy for PR. * Extra include file. * Extra library * Tidy forward declarations. * Don't prune if threshold < 0.0. * Windows exporty thing. * Check SMILES on merge of ShapeInputs. * PRECONDITION of SMILES on merge of ShapeInputs. * Response to review - rename some functions. * change how overlapVols is passed add a test for it * API suggestions * Response to review. * Remove debugging writes. * Fix Python wrappers. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: greg landrum <greg.landrum@gmail.com>
RDKit
What is it?
The 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
- JavaScript (generated with emscripten) and CFFI wrappers around important functionality
- 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
Installation and getting started
If you are working in Python and using conda (our recommendation), installation is super easy:
$ conda install -c conda-forge rdkit
You can then take a look at our Getting Started in Python guide.
More detailed installation instructions are available in Docs/Book/Install.md.
Documentation
Available on the RDKit page and in the Docs folder on GitHub
The RDKit blog often has useful tips and tricks.
Support and Community
If you have questions, comments, or suggestions, the best places for those are:
If you've found a bug or would like to request a feature, please create an issue
We also have a LinkedIn group
We have a yearly user group meeting (the UGM) where members of the community do presentations and lightning talks on things they've done with the RDKit. Materials from past UGMs, which can quite useful, are also online:
- 2012 UGM, London
- 2013 UGM, Hinxton
- 2014 UGM, Darmstadt
- 2015 UGM, Zurich
- 2016 UGM, Basel
- 2017 UGM, Berlin
- 2018 UGM, Cambridge
- 2019 UGM, Hamburg
- 2020 UGM, virtual
- 2021 UGM, virtual
- 2022 UGM, Berlin
- 2023 UGM, Mainz
- 2024 UGM, Zurich
License
Code released under the BSD license.