Cocktail Shaker
Cocktail Shaker: An open source drug expansion and enumeration library for peptides - Published in JOSS (2020)
Science Score: 93.0%
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Found 1 DOI reference(s) in JOSS metadata -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Repository
A peptide string building for expanding chemical dataset combinations.
Basic Info
Statistics
- Stars: 12
- Watchers: 3
- Forks: 6
- Open Issues: 95
- Releases: 5
Metadata Files
README.md
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.
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 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.
- 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.
External links
Owner
- Name: Sul
- Login: Sulstice
- Kind: user
- Location: United States
- Company: @mackerell-lab
- Website: https://twitter.com/SulimanSharif6
- Twitter: SulimanSharif6
- Repositories: 129
- Profile: https://github.com/Sulstice
I'm a PhD Scientist who loves organic chemistry, devops, chemicals, social media, stock marketing, art, and law. I try to develop in those areas.
JOSS Publication
Cocktail Shaker: An open source drug expansion and enumeration library for peptides
Authors
None
Editor
Charlotte Soneson
Tags
Cheminformatics RDKit PeptidesGitHub Events
Total
- Watch event: 2
- Delete event: 10
- Issue comment event: 10
- Push event: 11
- Pull request event: 20
- Create event: 12
Last Year
- Watch event: 2
- Delete event: 10
- Issue comment event: 10
- Push event: 11
- Pull request event: 20
- Create event: 12
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| sulimansharif | s****1@g****m | 189 |
| RoseGierth722 | 5****2 | 18 |
| Suliman Sharif | s****f@S****l | 7 |
| Charlotte Soneson | c****n@g****m | 3 |
| Marvin | c****n@g****m | 2 |
| pyup-bot | g****t@p****o | 2 |
| Charles Tapley Hoyt | c****t@g****m | 2 |
| dependabot[bot] | d****] | 1 |
| The Gitter Badger | b****r@g****m | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 333
- Average time to close issues: N/A
- Average time to close pull requests: 3 months
- Total issue authors: 0
- Total pull request authors: 4
- Average comments per issue: 0
- Average comments per pull request: 0.81
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 8
Past Year
- Issues: 0
- Pull requests: 31
- Average time to close issues: N/A
- Average time to close pull requests: 25 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.48
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Sulstice (1)
Pull Request Authors
- pyup-bot (418)
- Sulstice (27)
- dependabot[bot] (8)
- snyk-bot (4)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 30 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 13
- Total maintainers: 1
pypi.org: cocktail-shaker
- Homepage: https://www.github.com/Sulstice/Cocktail-Shaker
- Documentation: https://cocktail-shaker.readthedocs.io/
- License: MIT
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Latest release: 1.1.8
published over 5 years ago
Rankings
Maintainers (1)
Dependencies
- Babel ==2.7.0
- Jinja2 ==2.10.3
- MarkupSafe ==1.1.1
- MolVS ==0.1.1
- Pygments ==2.4.2
- Sphinx ==2.2.1
- alabaster ==0.7.12
- attrs ==19.3.0
- certifi ==2019.9.11
- chardet ==3.0.4
- idna ==2.8
- imagesize ==1.1.0
- importlib-metadata ==0.23
- lxml ==4.4.1
- more-itertools ==7.2.0
- numpy ==1.17.3
- packaging ==19.2
- pandas ==0.25.3
- py ==1.8.0
- pyOpenSSL ==19.1.0
- pyparsing ==2.4.5
- pytest ==5.3.0
- python-dateutil ==2.8.1
- python-utils ==2.3.0
- pytz ==2019.3
- requests ==2.22.0
- ruamel.yaml ==0.16.5
- ruamel.yaml.clib ==0.2.0
- six ==1.13.0
- snowballstemmer ==2.0.0
- sphinx-bootstrap-theme ==0.7.1
- urllib3 ==1.25.7
- wcwidth ==0.1.7
- zipp ==0.6.0