Metadata-Version: 2.1
Name: equilibrator-api
Version: 0.4.1
Summary: Calculation of standard thermodynamic potentials of biochemical reactions.
Home-page: https://gitlab.com/equilibrator/equilibrator-api/
Author: Elad Noor, Moritz E. Beber
Author-email: eladn@weizmann.ac.il, midnighter@posteo.net
License: MIT
Download-URL: https://pypi.org/project/equilibrator-api/
Project-URL: Source Code, https://gitlab.com/equilibrator/equilibrator-api/
Project-URL: Bug Tracker, https://gitlab.com/equilibrator/equilibrator-api/-/issues
Description: # eQuilibrator - a thermodynamics calculator for biochemical reactions
        
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        ## What is `equilibrator-api`?
        
        `equilibrator-api` is a Python package for obtaining estimates of reactions Gibbs energies.
        It is mainly meant for biologists/bioengineers with basic programming skills that
        work on metabolism and want to easily add thermodynamic data to their models.
        
        The documentation is browseable online at
        [readthedocs](https://equilibrator.readthedocs.io/en/latest/index.html).
        
        If your list of reactions is very short, we recommend trying our
        website called [eQuilibrator](http://equilibrator.weizmann.ac.il/) before spending
        the time necessary for learning how to use `equilibrator-api`.
        
        The main advantages of `equilibrator-api` are:
        
        * Batch mode: can be used for large reaction datasets (even more than 1000 reactions)
        * Does not require a network connection (except during installation and initialization)
        * Works with standard compound identifiers (such as ChEBI, KEGG, BiGG and MetaNetX) for more than 500,000 compounds
        
        To access more advanced features, such as adding new compounds that are not
        among the 500,000 currently in the MetaNetX database, try using our 
        [equilibrator-assets](https://gitlab.com/equilibrator/equilibrator-assets)
        package.
        
        ## Cite us
        
        If you plan to use results from `equilibrator-api` in a scientific publication,
        please cite our 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
        
        ## A very simple example
        
        Note that creating a `ComponentContribution` object for the first time after
        installation, starts an initialization step which downloads ~1.5 GBytes of data
        to your computer. It can take more than an hour (depending on the connection speed).
        The initialization **will not work inside a Jupyter notebook** environment - 
        you must run it in a standard python shell first.
        
        ```python
        from equilibrator_api import ComponentContribution
        cc = ComponentContribution()
        rxn = cc.parse_reaction_formula("kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009")
        print(f"ΔG'0 = {cc.standard_dg_prime(rxn)}")
        ```
        
Keywords: component contribution,Gibbs energy,biochemical reaction,eQuilibrator
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
Provides-Extra: test
Provides-Extra: development
Provides-Extra: deployment
