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README
README.md
1# RDKit
2[![Azure build Status](https://dev.azure.com/rdkit-builds/RDKit/_apis/build/status/rdkit.rdkit?branchName=master)](https://dev.azure.com/rdkit-builds/RDKit/_build/latest?definitionId=1&branchName=master)
3[![Documentation Status](https://readthedocs.org/projects/rdkit/badge/?version=latest)](http://rdkit.readthedocs.org/en/latest/)
4[![DOI](https://zenodo.org/badge/10009991.svg)](https://zenodo.org/badge/latestdoi/10009991)
5
6
7[RDKit](https://github.com/rdkit/rdkit) is a collection of cheminformatics and machine-learning software written in C++ and Python.
8
9 * [BSD license](https://github.com/rdkit/rdkit/blob/master/license.txt) - a business friendly license for open source
10 * Core data structures and algorithms in C++
11 * [Python 3.x wrapper](https://www.rdkit.org/docs/GettingStartedInPython.html) generated using Boost.Python
12 * Java and C# wrappers generated with SWIG
13 * 2D and 3D molecular operations
14 * [Descriptor](https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors) and [Fingerprint](http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-fingerprints) generation for machine learning
15 * Molecular database [cartridge](https://www.rdkit.org/docs/Cartridge.html) for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
16 * Cheminformatics nodes for [KNIME](https://www.knime.com/rdkit)
17 * [Contrib](https://github.com/rdkit/rdkit/tree/master/Contrib) folder with useful community-contributed software harnessing the power of the RDKit
18
19#### Community
20
21 * [Mailing list](https://sourceforge.net/p/rdkit/mailman/)
22 * [GitHub discussions](https://github.com/rdkit/rdkit/discussions)
23 * [LinkedIn](https://www.linkedin.com/groups/RDKit-8192558/about)
24
25#### Code
26
27 * [GitHub code](https://github.com/rdkit) and [bug tracker](https://github.com/rdkit/rdkit/issues)
28
29## Web presence
30
31 * [RDKit web page](https://rdkit.org)
32 * [Blog](https://rdkit.blogspot.com)
33 * [Documentation](https://www.rdkit.org/docs/index.html)
34
35#### Materials from user group meetings
36
37 * [2012 UGM](http://www.rdkit.org/UGM/2012/)
38 * [2013 UGM](https://github.com/rdkit/UGM_2013)
39 * [2014 UGM](https://github.com/rdkit/UGM_2014)
40 * [2015 UGM](https://github.com/rdkit/UGM_2015)
41 * [2016 UGM](https://github.com/rdkit/UGM_2016)
42 * [2017 UGM](https://github.com/rdkit/UGM_2017)
43 * [2018 UGM](https://github.com/rdkit/UGM_2018)
44 * [2019 UGM](https://github.com/rdkit/UGM_2019)
45 * [2020 UGM](https://github.com/rdkit/UGM_2020)
46
47## Documentation
48Available on the [RDKit page](https://www.rdkit.org/docs/index.html)
49and in the [Docs](https://github.com/rdkit/rdkit/tree/master/Docs) folder on GitHub
50
51## Installation
52
53Installation instructions are available in [Docs/Book/Install.md](https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md).
54
55#### Binary distributions, anaconda, homebrew
56
57 * [binaries for conda python](https://anaconda.org/rdkit/rdkit) or, if you are using the conda-forge stack, the RDKit is also [available from conda-forge](https://anaconda.org/conda-forge/rdkit).
58 * [RPMs](https://src.fedoraproject.org/rpms/rdkit) for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
59 * [debs](https://blends.debian.org/debichem/tasks/cheminformatics) for Ubuntu and other Debian-derived Linux distros. Contributed by the Debichem team.
60 * [homebrew](https://github.com/rdkit/homebrew-rdkit) formula for building on the Mac. Contributed by Eddie Cao.
61 * [recipes](https://github.com/rdkit/conda-rdkit) for building using the excellent conda package manager. Contributed by Riccardo Vianello.
62 * [APKs](https://github.com/daverona/alpine-rdkit) for Alpine Linux. Contributed by da Verona
63
64## Projects using RDKit
65
66- [Scopy](https://github.com/kotori-y/Scopy) ([docs](https://scopy.iamkotori.com/), [paper](https://doi.org/10.1093/bib/bbaa194)) - an integrated negative design Python library for desirable HTS/VS database design
67- [stk](https://github.com/lukasturcani/stk) ([docs](https://stk.readthedocs.io), [paper](https://onlinelibrary.wiley.com/doi/10.1002/jcc.25377)) -
68a Python library for building, manipulating, analyzing and automatic design of molecules.
69- [gpusimilarity](https://github.com/schrodinger/gpusimilarity) - A Cuda/Thrust implementation of fingerprint similarity searching
70- [Samson Connect](https://www.samson-connect.net) - Software for adaptive modeling and simulation of nanosystems
71- [mol_frame](https://github.com/apahl/mol_frame) - Chemical Structure Handling for Dask and Pandas DataFrames
72- [RDKitjs](https://github.com/cheminfo/RDKitjs) - port of RDKit functionality to JavaScript
73- [DeepChem](https://deepchem.io) - python library for deep learning for chemistry
74- [mmpdb](https://github.com/rdkit/mmpdb) - Matched molecular pair database generation and analysis
75- [CheTo](https://github.com/rdkit/CheTo) ([paper](http://pubs.acs.org/doi/10.1021/acs.jcim.7b00249))- Chemical topic modeling
76- [OCEAN](https://github.com/rdkit/OCEAN) ([paper](http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00067))- Optimized cross reactivity estimation
77- [ChEMBL Beaker](https://github.com/mnowotka/chembl_beaker) - standalone web server wrapper for RDKit and OSRA
78- [myChEMBL](https://github.com/chembl/mychembl) ([blog post](http://chembl.blogspot.de/2013/10/chembl-virtual-machine-aka-mychembl.html), [paper](http://bioinformatics.oxfordjournals.org/content/early/2013/11/20/bioinformatics.btt666)) - A virtual machine implementation of open data and cheminformatics tools
79- [ZINC](http://zinc15.docking.org) - Free database of commercially-available compounds for virtual screening
80- [sdf_viewer.py](https://github.com/apahl/sdf_viewer) - an interactive SDF viewer
81- [sdf2ppt](https://github.com/dkuhn/sdf2ppt) - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
82- [MolGears](https://github.com/admed/molgears) - A cheminformatics tool for bioactive molecules
83- [PYPL](http://www.biochemfusion.com/downloads/#OracleUtilities) - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
84- [shape-it-rdkit](https://github.com/jandom/shape-it-rdkit) - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
85- [WONKA](http://wonka.sgc.ox.ac.uk/WONKA/) - Tool for analysis and interrogation of protein-ligand crystal structures
86- [OOMMPPAA](http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/) - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
87- [OCEAN](https://github.com/rdkit/OCEAN) - web-tool for target-prediction of chemical structures which uses ChEMBL as datasource
88- [chemfp](http://chemfp.com) - very fast fingerprint searching
89- [rdkit_ipynb_tools](https://github.com/apahl/rdkit_ipynb_tools) - RDKit Tools for the IPython Notebook
90- [Vernalis KNIME nodes](https://www.knime.com/book/vernalis-nodes-for-knime-trusted-extension)
91- [Erlwood KNIME nodes](https://www.knime.com/community/erlwood)
92- [AZOrange](https://github.com/AZcompTox/AZOrange)
93
94## License
95
96Code released under the [BSD license](https://github.com/rdkit/rdkit/blob/master/license.txt).
97