Metadata-Version: 2.1
Name: cocktail-shaker
Version: 1.1.0
Summary: UNKNOWN
Home-page: https://www.github.com/Sulstice/Cocktail-Shaker
Author: Suliman Sharif
Author-email: sharifsuliman1@gmail.com
License: MIT
Description: Cocktail Shaker: Drug Expansion and Enumeration for Peptides!
        =============================================================
        
        [![Build](https://travis-ci.org/Sulstice/Cocktail-Shaker.svg?branch=master)](https://travis-ci.org/Sulstice/Cocktail-Shaker)
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        <p align="center">
          <img width="200" height="300" src="images/logoshaker.png">
        </p>
        
        cocktail-shaker is a **high-performance drug enumeration and expansion
        library**. cocktail-shaker leverages the computational power of
        **RDKit** to create and enumerate large volumes of drug compounds. 
        - File parsing of SDF
        - File writing in a variety of formats some of which include: cif, sdf, pdb, mol, mol2, and more.
        - Ability to recognize and expand libraries of compounds some of which include: halogens, acyl halides, aldehydes. 
        - Ability to enumerate in 1D and 2D structures and produce those compounds.
        
        Announcements
        =============
        
        -   **Release!** Version 1.0.0-beta, August 26, 2019
        -   **RDkit UGM 2019**: talk at September 25th at the University of
            Hamburg, Germany.
        
        Using Cocktail Shaker
        =====================
        
        cocktail-shaker is a young library under heavy development at this time.
        It targets two categories of users:
        
        1.  **Users familiar with RDKit**, or those willing to learn RDKit, who want to
            create fast sets of data for high throughput screening or machine
            learning.
        2.  **Open-Science Scientists without any knowledge of RDKit** who are
            seeking a a high-level wrapper to create chemical files for their
            software.
        
        If you're in the first category, then you can already start using RDKit.
        cocktail-shaker offers a Pythonic, easy-to-use library and you can start
        channeling molecules in the expansion library. Instead of validating the
        sanity of the data, cocktail-shaker takes care of that for you. With
        each molecule being generated it will head into a 1D and/or 2D
        validation check (3D not supported yet).
        
        If you're in the second category, we're starting to build experimental
        high-level python code to take care a lot of the underpinnings of RDKit.
        
        Installation 
        ==================
        
        cocktail-shaker runs on Python 3.5+ and depends on RDKit version (make sure you have this installed!).
        
        To setup and install a conda env on the MacOS/Linux, first download Conda:
        
        Linux: 
        ``` $ wget/curl http://repo.continuum.io/miniconda/Miniconda3-4.1.11-Linux-x86_64.sh -O miniconda.sh ```
        
        MacOSx:
        ``` $ curl http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh ```
        
        Run the Installation:
        
        ``` $ sh Miniconda3-latest-MacOSX-x86_64.sh ```
        
        Create a conda environment: 
        
        ``` $ /anaconda3/bin/conda create -n your_env_name python=3.5 anaconda ```
        
        To install RDKit, set up an environment through this:
        
        ``` $ conda install -q -c rdkit rdkit ```
        
        cocktail-shaker can be installed either via \`pip\`:
        
        ``` $ your_env_name/bin/python -m pip install cocktail-shaker```
        
        Development Installation
        ========================
        
        As cocktail-shaker is under heavy development at this time, we highly
        recommend developers to use the development version on Github (master
        branch). You need to clone the repository and install cocktail-shaker with
        
        `python setup.py install`.
        
        As a one-liner, assuming git is installed:
        
            git clone https://github.com/Sulstice/Cocktail-Shaker.git
        
        This will automatically install the latest version of cocktail-shaker.
        
        Structure of cocktail-shaker
        ============================
        
        Currently, the main subpackages are:
        
        -   **cocktail_shaker**: Contains a lot of the high level functionality; request
            handling, file parsing/writing, enumeration, and expansion.
        -   **docs**: An access point for the readthedocs implementation.
        -   **cocktail_shaker/datasources**: This is where the system stores its data on
            predfined functional groups and/or shapes (coming soon).
        -   **tests**: Tests that are for the file handling, requests, and
            testing molecule pattern recognition.
        
        The API of all public interfaces are subject to change in the future,
        although **datasources** are *relatively* stable at this point.
        
        Genesis
        =======
        
        cocktail-shaker began when one developer/scientist wanted an open source
        drug library.
        
        - Lead Developer [Suliman sharif](http://sulstice.github.io/)
        - Artwork [Elena Chow](http://www.chowelena.com/)
        - Technical Documentation [Rose Gierth](https://www.linkedin.com/in/rose-gierth-69a4a083/)
        - QA Tester [Marvin Corro](https://www.linkedin.com/in/marvincorro/)
        
        Now cocktail-shaker looks to build on the expertise of these
        developers/scientists and the broader open-science community to build an
        effective drug library.
        
        * * * * *
        
        External links
        ==============
        
        -   [Documentation](http://cocktail-shaker.readthedocs.org)
        
        
Keywords: cocktail chemistry ligand-design shaker
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
