{ "info": { "author": "Suliman Sharif", "author_email": "sharifsuliman1@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7" ], "description": "Cocktail Shaker: Drug Expansion and Enumeration!\n================================================\n\n[![Build](https://travis-ci.org/Sulstice/Cocktail-Shaker.svg?branch=master)](https://travis-ci.org/Sulstice/Cocktail-Shaker)\n[![LICENSE](https://img.shields.io/badge/license-new%20BSD-blue.svg)](https://github.com/Sulstice/Cocktail-Shaker/blob/master/LICENSE)\n[![Coverage](https://coveralls.io/repos/github/Sulstice/Cocktail-Shaker/badge.svg?branch=master)](https://coveralls.io/github/Sulstice/Cocktail-Shaker?branch=master)\n![Python](https://img.shields.io/badge/python-3.6-blue.svg)\n[![Gitter](https://badges.gitter.im/Cocktail-Shaker/community.svg)](https://gitter.im/Cocktail-Shaker/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)\n[![Zenodo](https://zenodo.org/badge/170644606.svg)](https://zenodo.org/badge/latestdoi/170644606)\n[![Documentation Status](https://readthedocs.org/projects/cocktail-shaker/badge/?version=latest)](https://cocktail-shaker.readthedocs.io/en/latest/?badge=latest)\n\n

\n \n

\n\ncocktail-shaker is a **high-performance drug enumeration and expansion\nlibrary**. cocktail-shaker leverages the computational power of\n**RDKit** to create and enumerate large volumes of drug compounds. \n-File parsing of TXT, SDF, and Chemical SMILES.\n- File writing in a variety of formats some of which include: cif, sdf, pdb, mol, mol2, and more.\n- Ability to recognize and expand libraries of compounds some of which include: halogens, acyl halides, aldehydes. \n- Ability to enumerate in 1D and 2D structures and produce those compounds.\n\nAnnouncements\n=============\n\n- **Release!** Version 1.0.0-beta, August 26, 2019\n- **RDkit UGM 2019**: talk at September 25th at the University of\n Hamburg, Germany.\n\nUsing Cocktail Shaker\n=====================\n\ncocktail-shaker is a young library under heavy development at this time.\nIt targets two categories of users:\n\n1. **Users familiar with RDKit**, or those willing to learn RDKit, who want to\n create fast sets of data for high throughput screening or machine\n learning.\n2. **Open-Science Scientists without any knowledge of RDKit** who are\n seeking a a high-level wrapper to create chemical files for their\n software.\n\nIf you're in the first category, then you can already start using RDKit.\ncocktail-shaker offers a Pythonic, easy-to-use library and you can start\nchanneling molecules in the expansion library. Instead of validating the\nsanity of the data, cocktail-shaker takes care of that for you. With\neach molecule being generated it will head into a 1D and/or 2D\nvalidation check (3D not supported yet).\n\nIf you're in the second category, we're starting to build experimental\nhigh-level python code to take care a lot of the underpinnings of RDKit.\n\nInstallation \n==================\n\ncocktail-shaker runs on Python 3.5+ and depends on RDKit version (make sure you have this installed!).\n\nTo setup and install a conda env on the MacOS/Linux, first download Conda:\n\nLinux: \n``` $ wget/curl http://repo.continuum.io/miniconda/Miniconda3-4.1.11-Linux-x86_64.sh -O miniconda.sh ```\n\nMacOSx:\n``` $ curl http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh ```\n\nRun the Installation:\n\n``` $ sh Miniconda3-latest-MacOSX-x86_64.sh ```\n\nCreate a conda environment: \n\n``` $ /anaconda3/bin/conda create -n your_env_name python=3.5 anaconda ```\n\nTo install RDKit, set up an environment through this:\n\n``` $ conda install -q -c rdkit rdkit ```\n\ncocktail-shaker can be installed either via \\`pip\\`:\n\n``` $ your_env_name/bin/python -m pip install cocktail-shaker```\n\nDevelopment Installation\n========================\n\nAs cocktail-shaker is under heavy development at this time, we highly\nrecommend developers to use the development version on Github (master\nbranch). You need to clone the repository and install cocktail-shaker with\n\n`python setup.py install`.\n\nAs a one-liner, assuming git is installed:\n\n git clone https://github.com/Sulstice/Cocktail-Shaker.git\n\nThis will automatically install the latest version of cocktail-shaker.\n\nStructure of cocktail-shaker\n============================\n\nCurrently, the main subpackages are:\n\n- **cocktail_shaker**: Contains a lot of the high level functionality; request\n handling, file parsing/writing, enumeration, and expansion.\n- **docs**: An access point for the readthedocs implementation.\n- **cocktail_shaker/datasources**: This is where the system stores its data on\n predfined functional groups and/or shapes (coming soon).\n- **tests**: Tests that are for the file handling, requests, and\n testing molecule pattern recognition.\n\nThe API of all public interfaces are subject to change in the future,\nalthough **datasources** are *relatively* stable at this point.\n\nGenesis\n=======\n\ncocktail-shaker began when one developer/scientist wanted an open source\ndrug library.\n\n- Lead Developer [Suliman sharif](http://sulstice.github.io/)\n- Artwork [Elena Chow](http://www.chowelena.com/)\n- Technical Documentation [Rose Gierth](https://www.linkedin.com/in/rose-gierth-69a4a083/)\n- QA Tester [Marvin Corro](https://www.linkedin.com/in/marvincorro/)\n\nNow cocktail-shaker looks to build on the expertise of these\ndevelopers/scientists and the broader open-science community to build an\neffective drug library.\n\n* * * * *\n\nExternal links\n==============\n\n- [Documentation](http://cocktail-shaker.readthedocs.org)", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://www.github.com/Sulstice/Cocktail-Shaker", "keywords": "cocktail chemistry ligand-design shaker", "license": "MIT", "maintainer": "", "maintainer_email": "", 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