--- a/README.md +++ b/README.md @@ -1,75 +1,74 @@ -# 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 - -[](http://oddt.readthedocs.org/en/latest/) -[](https://travis-ci.org/oddt/oddt) -[](https://coveralls.io/github/oddt/oddt?branch=master) -[](https://landscape.io/github/oddt/oddt/master) -[](https://anaconda.org/oddt/oddt) -[](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) - - -[](https://github.com/igrigorik/ga-beacon) +# 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 + +[](http://oddt.readthedocs.org/en/latest/) +[](https://travis-ci.org/oddt/oddt) +[](https://coveralls.io/github/oddt/oddt?branch=master) +[](https://landscape.io/github/oddt/oddt/master) +[](https://anaconda.org/oddt/oddt) +[](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) + +