
# Open Drug Discovery Toolkit

Open 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

[![Documentation Status](https://readthedocs.org/projects/oddt/badge/?version=latest)](http://oddt.readthedocs.org/en/latest/)
[![Build Status](https://travis-ci.org/oddt/oddt.svg?branch=master)](https://travis-ci.org/oddt/oddt)
[![Coverage Status](https://coveralls.io/repos/github/oddt/oddt/badge.svg?branch=master)](https://coveralls.io/github/oddt/oddt?branch=master)
[![Code Health](https://landscape.io/github/oddt/oddt/master/landscape.svg?style=flat)](https://landscape.io/github/oddt/oddt/master)
[![Conda packages](https://anaconda.org/oddt/oddt/badges/version.svg?style=flat)](https://anaconda.org/oddt/oddt)
[![Latest Version](https://img.shields.io/pypi/v/oddt.svg)](https://pypi.python.org/pypi/oddt/)

## Documentation, Discussion and Contribution:
  * Documentation: http://oddt.readthedocs.org/en/latest
  * Mailing list: oddt@googlegroups.com  http://groups.google.com/d/forum/oddt
  * Issues: https://github.com/oddt/oddt/issues

## Requirements
  * Python 3.6+
  * OpenBabel (3.0+) or/and RDKit (2018.03+)
  * Numpy (1.12+)
  * Scipy (0.19+)
  * Sklearn (0.18+)
  * joblib (0.10+)
  * pandas (0.19.2+)
  * Skimage (0.12.3+) (optional, only for surface generation)

## Install

### Using PyPi (pip)
  When all requirements are met, then installation process is simple
  > python setup.py install

  You can also use pip. All requirements besides toolkits (OpenBabel, RDKit) are installed if necessary.
  Installing inside virtualenv is encouraged, but not necessary.
  > pip install oddt

  To upgrade oddt using pip (without upgrading dependencies):
  > pip install -U --no-deps oddt

### Using conda
  Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one.

  Install ODDT:
  > conda install -c oddt oddt

  You can add a toolkit of your choice or install them along with oddt:
  > conda install -c conda-forge oddt rdkit openbabel

  (Optionally) Install OpenBabel (using [official  channel](https://anaconda.org/openbabel/openbabel)):
  > conda install -c conda-forge openbabel

  (Optionally) Install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)):
  > conda install -c conda-forge rdkit

  Upgrading procedure using conda is straightforward:
  > conda update -c oddt oddt

### Documentation
Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally, it can be build locally:
   > cd docs

   > make html

   > make latexpdf

### License
ODDT is released under permissive [3-clause BSD license](./LICENSE)

### Reference
If you found Open Drug Discovery Toolkit useful for your research, please cite us!

1. 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)




	a/README.md		b/README.md
1	# Open Drug Discovery Toolkit	1	# Open Drug Discovery Toolkit
2		2
3	Open 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	3	Open 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		4
5	[![Documentation Status](https://readthedocs.org/projects/oddt/badge/?version=latest)](http://oddt.readthedocs.org/en/latest/)	5	[![Documentation Status](https://readthedocs.org/projects/oddt/badge/?version=latest)](http://oddt.readthedocs.org/en/latest/)
6	[![Build Status](https://travis-ci.org/oddt/oddt.svg?branch=master)](https://travis-ci.org/oddt/oddt)	6	[![Build Status](https://travis-ci.org/oddt/oddt.svg?branch=master)](https://travis-ci.org/oddt/oddt)
7	[![Coverage Status](https://coveralls.io/repos/github/oddt/oddt/badge.svg?branch=master)](https://coveralls.io/github/oddt/oddt?branch=master)	7	[![Coverage Status](https://coveralls.io/repos/github/oddt/oddt/badge.svg?branch=master)](https://coveralls.io/github/oddt/oddt?branch=master)
8	[![Code Health](https://landscape.io/github/oddt/oddt/master/landscape.svg?style=flat)](https://landscape.io/github/oddt/oddt/master)	8	[![Code Health](https://landscape.io/github/oddt/oddt/master/landscape.svg?style=flat)](https://landscape.io/github/oddt/oddt/master)
9	[![Conda packages](https://anaconda.org/oddt/oddt/badges/version.svg?style=flat)](https://anaconda.org/oddt/oddt)	9	[![Conda packages](https://anaconda.org/oddt/oddt/badges/version.svg?style=flat)](https://anaconda.org/oddt/oddt)
10	[![Latest Version](https://img.shields.io/pypi/v/oddt.svg)](https://pypi.python.org/pypi/oddt/)	10	[![Latest Version](https://img.shields.io/pypi/v/oddt.svg)](https://pypi.python.org/pypi/oddt/)
11		11
12	## Documentation, Discussion and Contribution:	12	## Documentation, Discussion and Contribution:
13	* Documentation: http://oddt.readthedocs.org/en/latest	13	* Documentation: http://oddt.readthedocs.org/en/latest
14	* Mailing list: oddt@googlegroups.com http://groups.google.com/d/forum/oddt	14	* Mailing list: oddt@googlegroups.com http://groups.google.com/d/forum/oddt
15	* Issues: https://github.com/oddt/oddt/issues	15	* Issues: https://github.com/oddt/oddt/issues
16		16
17	## Requirements	17	## Requirements
18	* Python 3.6+	18	* Python 3.6+
19	* OpenBabel (3.0+) or/and RDKit (2018.03+)	19	* OpenBabel (3.0+) or/and RDKit (2018.03+)
20	* Numpy (1.12+)	20	* Numpy (1.12+)
21	* Scipy (0.19+)	21	* Scipy (0.19+)
22	* Sklearn (0.18+)	22	* Sklearn (0.18+)
23	* joblib (0.10+)	23	* joblib (0.10+)
24	* pandas (0.19.2+)	24	* pandas (0.19.2+)
25	* Skimage (0.12.3+) (optional, only for surface generation)	25	* Skimage (0.12.3+) (optional, only for surface generation)
26		26
27	## Install	27	## Install
28		28
29	### Using PyPi (pip)	29	### Using PyPi (pip)
30	When all requirements are met, then installation process is simple	30	When all requirements are met, then installation process is simple
31	> python setup.py install	31	> python setup.py install
32		32
33	You can also use pip. All requirements besides toolkits (OpenBabel, RDKit) are installed if necessary.	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.	34	Installing inside virtualenv is encouraged, but not necessary.
35	> pip install oddt	35	> pip install oddt
36		36
37	To upgrade oddt using pip (without upgrading dependencies):	37	To upgrade oddt using pip (without upgrading dependencies):
38	> pip install -U --no-deps oddt	38	> pip install -U --no-deps oddt
39		39
40	### Using conda	40	### Using conda
41	Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one.	41	Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one.
42		42
43	Install ODDT:	43	Install ODDT:
44	> conda install -c oddt oddt	44	> conda install -c oddt oddt
45		45
46	You can add a toolkit of your choice or install them along with oddt:	46	You can add a toolkit of your choice or install them along with oddt:
47	> conda install -c conda-forge oddt rdkit openbabel	47	> conda install -c conda-forge oddt rdkit openbabel
48		48
49	(Optionally) Install OpenBabel (using [official channel](https://anaconda.org/openbabel/openbabel)):	49	(Optionally) Install OpenBabel (using [official channel](https://anaconda.org/openbabel/openbabel)):
50	> conda install -c conda-forge openbabel	50	> conda install -c conda-forge openbabel
51		51
52	(Optionally) Install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)):	52	(Optionally) Install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)):
53	> conda install -c conda-forge rdkit	53	> conda install -c conda-forge rdkit
54		54
55	Upgrading procedure using conda is straightforward:	55	Upgrading procedure using conda is straightforward:
56	> conda update -c oddt oddt	56	> conda update -c oddt oddt
57		57
58	### Documentation	58	### Documentation
59	Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally, it can be build locally:	59	Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally, it can be build locally:
60	> cd docs	60	> cd docs
61		61
62	> make html	62	> make html
63		63
64	> make latexpdf	64	> make latexpdf
65		65
66	### License	66	### License
67	ODDT is released under permissive [3-clause BSD license](./LICENSE)	67	ODDT is released under permissive [3-clause BSD license](./LICENSE)
68		68
69	### Reference	69	### Reference
70	If you found Open Drug Discovery Toolkit useful for your research, please cite us!	70	If you found Open Drug Discovery Toolkit useful for your research, please cite us!
71		71
72	1. 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)	72	1. 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		73
74		74
75	[![Analytics](https://ga-beacon.appspot.com/UA-44788495-3/oddt/oddt?flat)](https://github.com/igrigorik/ga-beacon)