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PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS\n\n[![GitHub Actions Build Status](https://github.com/radifar/PyPLIF-HIPPOS/workflows/CI/badge.svg)](https://github.com/radifar/PyPLIF-HIPPOS/actions?query=workflow%3ACI)\n[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/radifar/PyPLIF-HIPPOS.svg?logo=lgtm\u0026logoWidth=18)](https://lgtm.com/projects/g/radifar/PyPLIF-HIPPOS/context:python)\n[![codecov](https://codecov.io/gh/radifar/pyplif-hippos/branch/main/graph/badge.svg)](https://codecov.io/gh/radifar/pyplif-hippos/branch/main)   \n[![Anaconda-Server Badge](https://img.shields.io/badge/Install%20with-conda-green.svg?style=flat)](https://anaconda.org/conda-forge/pyplif-hippos)\n[![Documentation Status](https://readthedocs.org/projects/pyplif-hippos/badge/?version=latest\u0026style=flat)](https://pyplif-hippos.readthedocs.io/en/latest/)\n[![DOI:10.1021/acs.jcim.0c00305](https://zenodo.org/badge/DOI/10.1021/acs.jcim.0c00305.svg)](https://doi.org/10.1021/acs.jcim.0c00305)   \n[![Anaconda-Server Badge](https://img.shields.io/conda/dn/conda-forge/pyplif-hippos?color=green)](https://anaconda.org/conda-forge/pyplif-hippos)\n[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2Fradifar%2Fpyplif-hippos\u0026title=visitor%20today%2Ftotal)](https://hits.seeyoufarm.com)\n\n\u003cp align=\"center\"\u003e\n  \u003cimg alt=\"Icons made by Freepik from Flaticon is licensed by CC 3.0 BY\" src=\"docs/source/hippopotamus_small.png\"\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003eIcons made by \u003ca href=\"https://www.freepik.com/\"\u003eFreepik\u003c/a\u003e from \u003ca href=\"http://www.flaticon.com\"\u003eFlaticon\u003c/a\u003e is licensed by CC 3.0 BY\u003c/p\u003e\n\nWelcome to PyPLIF-HIPPOS's project page. PyPLIF-HIPPOS is an upgraded version of [PyPLIF](https://github.com/radifar/pyplif/) (**Python-based Protein-Ligand Interaction Fingerprinting**), a tool for molecular docking post-analysis. It will translate the 3D coordinates of both ligand(s) (generated from docking simulation) and protein into a series of *interaction bitstring* (also known as *Interaction Fingerprint*) (see image below). **HIPPOS** (/ˌhipoʊz/) is a recursive acronym of **HIPPOS Is PyPLIF On Steroids**. From this point forward, PyPLIF-HIPPOS is simplified to HIPPOS.\n\nCompared to PyPLIF, HIPPOS is not only faster and able to generate more customized interaction bitstring, but also supports both [PLANTS](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants/) \u0026 [Vina](http://vina.scripps.edu/)! More over, unlike its predecessor it is (far) more well-documented.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg alt=\"Table of Content Abstract Graphic JCIM\" src=\"docs/source/toc-abstract-graphics_small.png\"\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003eReprinted with permission from https://doi.org/10.1021/acs.jcim.0c00305. Copyright 2020 American Chemical Society.\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003cimg alt=\"PyPLIF output from PyPLIF publication\" src=\"docs/source/pyplif.png\"\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003eIllustration by Radifar et al (2013) from \u003ca href=\"http://www.bioinformation.net/009/97320630009325.htm\"\u003eBioinformation.net\u003c/a\u003e is licensed by \u003ca href=\"http://creativecommons.org/licenses/by/4.0\"\u003eCC 4.0 BY\u003c/a\u003e\n\n## Quick Installation\n\nThe easiest way to install HIPPOS is using [Anaconda or Miniconda](https://docs.anaconda.com/anaconda/install/).\nIf you have Anaconda or Miniconda ready in your machine, you can start with\ncreating new environment (recommended):\n\n`conda create -n hippos python=3.6`\n\nThen activate the environment and install HIPPOS:\n\n`conda activate hippos`  \n`conda install -c conda-forge pyplif-hippos`\n\nnext you can try run HIPPOS and HIPPOS-GENREF with the following command:\n\n`hippos`  \n`hippos-genref` \n\n## How to Use HIPPOS\n\nSo I already installed HIPPOS, now what? Well you could start with how to generate\nthe [reference bitstring](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-genref.html)\nand Getting Started tutorial for [AutoDock Vina](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-vina.html)\nor [PLANTS](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-plants.html).\n\n## Ideas for Improvement? Found Bug(s)?\n\nIf you have any idea for improvement or found bug to report feel free to write them [here](https://github.com/radifar/PyPLIF-HIPPOS/issues).\n\n## Citing HIPPOS\n\nIf you are using HIPPOS please cite this paper:\n\nIstyastono, E., Radifar, M., Yuniarti, N., Prasasty, V. and Mungkasi, S., 2020. \nPyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results \nof AutoDock Vina and PLANTS. Journal of Chemical Information and Modeling, 60(8), pp.3697-3702.\nhttps://doi.org/10.1021/acs.jcim.0c00305\n\n## Acknowledgment\n\nThis project has received funding from the [National Agency for Research and Innovation](https://international.ristekdikti.go.id/) (Indonesia)\nunder grant agreement No. 807.7/LL5/PG/2020. This project has been restructured based on the\n[MOLSSI Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms)\nversion 1.3, and benefited greatly from [MOLSSI Python Package Development Best Practices](https://molssi.org/2020/04/20/may-webinar-series-python-package-development/)\nworkshop.\n\n\n-----\n\n\u0026copy; Copyright 2021, Muhammad Radifar \u0026 Enade Perdana Istyastono\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fradifar%2Fpyplif-hippos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fradifar%2Fpyplif-hippos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fradifar%2Fpyplif-hippos/lists"}