Metadata-Version: 2.1
Name: component-contribution
Version: 0.4.1
Summary: Standard reaction Gibbs energy estimation for biochemical reactions.
Home-page: https://gitlab.com/equilibrator/component-contribution
Author: Elad Noor, Moritz E. Beber
Author-email: eladn@weizmann.ac.il, midnighter@posteo.net
License: MIT
Download-URL: https://pypi.org/project/component-contribution/
Project-URL: Source Code, https://gitlab.com/equilibrator/component-contribution
Project-URL: Bug Tracker, https://gitlab.com/equilibrator/component-contribution/-/issues
Keywords: component contribution,Gibbs energy,biochemical reaction,eQuilibrator,cache
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: equilibrator-cache (~=0.4.1)
Requires-Dist: path (~=15.0)
Requires-Dist: periodictable (~=1.5)
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Requires-Dist: httpx (~=0.16)
Requires-Dist: tenacity (~=6.2)
Provides-Extra: deployment
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Requires-Dist: click-log ; extra == 'deployment'
Requires-Dist: python-dateutil ; extra == 'deployment'
Requires-Dist: requests ; extra == 'deployment'
Requires-Dist: openbabel (>=3.0.0) ; extra == 'deployment'
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Provides-Extra: test
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Requires-Dist: pytest-raises ; extra == 'test'

# Component Contribution

[![pipeline status](https://gitlab.com/elad.noor/component-contribution/badges/develop/pipeline.svg)](https://gitlab.com/elad.noor/component-contribution/commits/develop)

[![coverage report](https://gitlab.com/elad.noor/component-contribution/badges/develop/coverage.svg)](https://gitlab.com/elad.noor/component-contribution/commits/develop)

[![Join the chat at https://gitter.im/equilibrator-devs/component-contribution](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/equilibrator-devs/component-contribution?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

A method for estimating the standard reaction Gibbs energy of biochemical reactions. 

## Cite us

For more information on the method behind component-contribution, please view our open
access paper:

Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013)
[Consistent Estimation of Gibbs Energy Using Component Contributions](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098),
PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098

Please, cite this paper if you publish work that uses `component-contribution`.

## Installation

* `pip install component-contribution`

## Dependencies

* Python 3.6+
* PyPI dependencies for prediction:
  - equilibrator-cache
  - numpy
  - scipy
  - pandas
  - python-Levenshtein-wheels
  - pint
  - path
  - appdirs
  - diskcache
  - httpx
  - tenacity
  - periodictable
  - uncertainties
  - pyzenodo3
* PyPI dependencies for training a new model:
  - openbabel
  - equilibrator-assets

## Data sources

* [Training data for the component contribution method](https://zenodo.org/record/3978440)
* [Chemical group definitions for the component-contribution method](https://zenodo.org/record/4010930)


