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Project description
Cocktail Shaker: Drug Expansion and Enumeration for Peptides!
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:
- 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.
- 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
- Artwork Elena Chow
- Technical Documentation Rose Gierth
- QA Tester Marvin Corro
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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