diff --git a/README.md b/README.md index 484b64d..c3dbdf6 100644 --- a/README.md +++ b/README.md @@ -1,50 +1,21 @@ +[![unittests](https://github.com/haddocking/prodigy-cryst/actions/workflows/unittests.yml/badge.svg)](https://github.com/haddocking/prodigy-cryst/actions/workflows/unittests.yml) [![codecov](https://codecov.io/gh/haddocking/prodigy-cryst/branch/master/graph/badge.svg?token=KCGiAqKRnu)](https://codecov.io/gh/haddocking/prodigy-cryst) -# Interface Classifier +# PRODIGY-cryst -Collection of scripts to predict whether an interface in a protein-protein -complex is biological or crystallographic from its atomic coordinates. +Collection of scripts to predict whether an interface in a protein-protein complex is biological or crystallographic from its atomic coordinates. -## Quick & Dirty Installation +## Installation ```bash -git clone http://github.com/biopython/biopython.git -cd biopython -sudo python setup.py install # Alternatively, install locally but fix $PYTHONPATH - -wget https://github.com/mittinatten/freesasa/releases/download/1.0/freesasa-1.0.tar.gz -tar -xzvf freesasa-1.0.tar.gz -cd freesasa-1.0 -./configure && make && make install - -pip3 install scikit-learn==0.22 - -git clone http://github.com/haddocking/interface-classifier - -# Edit the config.py to setup the paths to the freesasa binary and radii files - -# Have fun! +> git clone http://github.com/haddocking/prodigy-cryst +> python setup.py install ``` ## Usage ```bash -python interface_classifier.py [--selection ] +prodigy_cryst [--selection ] ``` -Type --help to get a list of all the possible options of the script. - -## Dependencies - -- The scripts rely on [Biopython](www.biopython.org) to validate the PDB structures and calculate interatomic distances. -- [freesasa](https://github.com/mittinatten/freesasa), with the parameter set used in NACCESS ([Chothia,1976](http://www.ncbi.nlm.nih.gov/pubmed/994183)), is also required for calculating the buried surface area. Both 2.x and 1.x version series are supported. -- [scikit-learn](https://github.com/scikit-learn/scikit-learn) for Python 3 is necessary to load and use the classifier. - -To install and use the scripts, just clone the git repository or download the tarball zip -archive. Make sure `freesasa`, Biopython and scikit-learn are accessible to the Python scripts -through the appropriate environment variables ($PYTHONPATH). - -## License - -These utilities are open-source and licensed under the Apache License 2.0. For more information -read the LICENSE file. +Type --help to get a list of all the possible options.