README.md
1# Open Drug Discovery Toolkit
2
3Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
4
5[](http://oddt.readthedocs.org/en/latest/)
6[](https://travis-ci.org/oddt/oddt)
7[](https://coveralls.io/github/oddt/oddt?branch=master)
8[](https://landscape.io/github/oddt/oddt/master)
9[](https://anaconda.org/oddt/oddt)
10[](https://pypi.python.org/pypi/oddt/)
11
12## Documentation, Discussion and Contribution:
13 * Documentation: http://oddt.readthedocs.org/en/latest
14 * Mailing list: oddt@googlegroups.com http://groups.google.com/d/forum/oddt
15 * Issues: https://github.com/oddt/oddt/issues
16
17## Requrements
18 * Python 2.7 or 3.5+
19 * OpenBabel (2.3.2+) or/and RDKit (2016.03)
20 * Numpy (1.11+)
21 * Scipy (0.17+)
22 * Sklearn (0.18+)
23 * joblib (0.9.4+)
24 * pandas (0.19.2+)
25 * Skimage (0.12.3+) (optional, only for surface generation)
26
27## Install
28
29### Using PyPi (pip)
30 When all requirements are met, then installation process is simple
31 > python setup.py install
32
33 You can also use pip. All requirements besides toolkits (OpenBabel, RDKit) are installed if necessary.
34 Installing inside virtualenv is encouraged, but not necessary.
35 > pip install oddt
36
37 To upgrade oddt using pip (without upgrading dependencies):
38 > pip install -U --no-deps oddt
39
40### Using conda
41 Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one.
42
43 Install ODDT:
44 > conda install -c oddt oddt
45
46 You can add a toolkit of your choice or install them along with oddt:
47 > conda install -c oddt oddt rdkit openbabel
48
49 (Optionally) Install OpenBabel (using [official channel](https://anaconda.org/openbabel/openbabel)):
50 > conda install -c openbabel openbabel
51
52 (Optionally) install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)):
53 > conda install -c rdkit rdkit
54
55 Upgrading procedure using conda is straightforward:
56 > conda update -c oddt oddt
57
58### Documentation
59Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally it can be build localy:
60 > cd docs
61
62 > make html
63
64 > make latexpdf
65
66### License
67ODDT is released under permissive [3-clause BSD license](./LICENSE)
68
69### Reference
70If you found Open Drug Discovery Toolkit useful for your research, please cite us!
71
721. Wójcikowski, M., Zielenkiewicz, P., & Siedlecki, P. (2015). Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. Journal of Cheminformatics, 7(1), 26. [doi:10.1186/s13321-015-0078-2](https://dx.doi.org/10.1186/s13321-015-0078-2)
73
74
75[](https://github.com/igrigorik/ga-beacon)
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