{
    "info": {
        "author": "C\u00e9dric Bouysset",
        "author_email": "bouysset.cedric@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry"
        ],
        "description": "[![PyPI - Version](https://badge.fury.io/py/prolif.svg)](https://pypi.org/project/prolif/)\n[![PyPI - License](https://img.shields.io/pypi/l/prolif.svg)](https://pypi.org/project/prolif/)\n[![PyPI - Status](https://img.shields.io/pypi/status/prolif.svg)](https://pypi.org/project/prolif/)\n[![Build Status](https://travis-ci.org/cbouy/ProLIF.svg?branch=master)](https://travis-ci.org/cbouy/ProLIF)\n[![Coveralls github branch](https://img.shields.io/coveralls/github/cbouy/ProLIF/master.svg)](https://coveralls.io/github/cbouy/ProLIF?branch=master)\n[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/cbouy)\n\n# ProLIF\nProtein-Ligand Interaction Fingerprints\n\n:warning: This project is under active development, and might be subject to drastic changes. Use at your own risks :warning:\n\n## Description\n\nProLIF is a tool designed to generate Interaction FingerPrints (IFP) and compute similarity scores for protein-ligand interactions, given a reference ligand and a list of binding-site residues.\n\n## Installation\n\nProLIF is written in Python 3, and uses the following non-standard libraries:\n* numpy\n* [rdkit](http://www.rdkit.org/docs/Install.html)\n\n\nMake sure RDKit is installed before proceeding to the next step:\n```\nconda install -c rdkit rdkit\n```\n\nOnce this is done, you can download the package with Pip:\n```\npip install prolif\n```\n\n## Usage\n\n```\nINPUT arguments:\n  -r fileName, --reference fileName\n                        Path to your reference ligand.\n  -l fileName [fileName ...], --ligand fileName [fileName ...]\n                        Path to your ligand(s).\n  -p fileName, --protein fileName\n                        Path to your protein.\n  --residues RESIDUES [RESIDUES ...]\n                        Residues chosen for the interactions. Default: automatically detect residues within --cutoff of the reference ligand\n  --cutoff float        Cutoff for automatic residue detection: distance between centroids. Default: 12.0 \u212b\n  --json fileName       Path to a custom parameters file. Default: /home/cedric/Dropbox/work/prolif/prolif/parameters.json\n\nOUTPUT arguments:\n  -o filename, --output filename\n                        Path to the output CSV file\n  --log level           Set the level of the logger. Default: ERROR\n  -v, --version         Show version and exit\n\nOther arguments:\n  --interactions bit [bit ...]\n                        List of interactions used to build the fingerprint.\n                                      \u2502          Class         Ligand        Residue\n                                      \u2502\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\u2015\n                              HBdonor \u2502  Hydrogen bond          donor       acceptor\n                           HBacceptor \u2502  Hydrogen bond       acceptor          donor\n                              XBdonor \u2502   Halogen bond          donor       acceptor\n                           XBacceptor \u2502   Halogen bond       acceptor          donor\n                               cation \u2502          Ionic         cation          anion\n                                anion \u2502          Ionic          anion         cation\n                          hydrophobic \u2502    Hydrophobic    hydrophobic    hydrophobic\n                           FaceToFace \u2502    Pi-stacking       aromatic       aromatic\n                           FaceToEdge \u2502    Pi-stacking       aromatic       aromatic\n                            pi-cation \u2502      Pi-cation       aromatic         cation\n                            cation-pi \u2502      Pi-cation         cation       aromatic\n                              MBdonor \u2502          Metal          metal         ligand\n                           MBacceptor \u2502          Metal         ligand          metal\n                        Default: HBdonor HBacceptor cation anion FaceToFace FaceToEdge hydrophobic\n  --score {tanimoto,dice,tversky}\n                        Similarity score between molecule A and B :\n                        Let 'a' and 'b' be the number of bits activated in molecules A and B, and 'c' the number of activated bits in common.\n                            -) tanimoto : c/(a+b-c). Used by default\n                            -) dice     : 2c/(a+b)\n                            -) tversky  : c/(alpha*(a-c)+beta*(b-c)+c)\n  --alpha int           Alpha parameter for Tversky. Default: 0.7\n  --beta int            Beta parameter for Tversky. Default: 0.3\n\nMandatory arguments: --reference --ligand --protein\nMOL2 files only.\n```\n\n## License\n\nUnless otherwise noted, all files in this directory and all subdirectories are distributed under the Apache License, Version 2.0:\n```\n   Copyright 2017-2018 C\u00e9dric BOUYSSET\n\n   Licensed under the Apache License, Version 2.0 (the \"License\");\n   you may not use this file except in compliance with the License.\n   You may obtain a copy of the License at\n\n       http://www.apache.org/licenses/LICENSE-2.0\n\n   Unless required by applicable law or agreed to in writing, software\n   distributed under the License is distributed on an \"AS IS\" BASIS,\n   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n   See the License for the specific language governing permissions and\n   limitations under the License.\n```",
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