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Cocktail Shaker: Drug Expansion and Enumeration for Peptides!

Build License: MPL 2.0 Coverage Python Gitter Zenodo Documentation Status status PEP8

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.

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

asciicast

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 within a conda environment due to the RDKit dependency. A conda installation is coming soon (as soon as I figure it out).

For the time being, here is the following:

Cocktail shaker is distributed through PyPi and can be installed via:

your_env/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.

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.


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