%global _empty_manifest_terminate_build 0 Name: python-equilibrator-api Version: 0.4.7 Release: 1 Summary: Calculation of standard thermodynamic potentials of biochemical reactions. License: MIT URL: https://gitlab.com/equilibrator/equilibrator-api/ Source0: https://mirrors.aliyun.com/pypi/web/packages/15/fc/4024b4ba267b0ca33fc065f080e15530bb55c6e029f26c3f63478b27b983/equilibrator-api-0.4.7.tar.gz BuildArch: noarch Requires: python3-pyparsing Requires: python3-slugify Requires: python3-equilibrator-cache Requires: python3-component-contribution Requires: python3-click Requires: python3-click-log Requires: python3-dateutil Requires: python3-requests Requires: python3-black Requires: python3-isort Requires: python3-safety Requires: python3-tox Requires: python3-twine Requires: python3-cobra Requires: python3-pytest Requires: python3-pytest-cov Requires: python3-pytest-raises Requires: python3-pytest-allclose Requires: python3-sbtab %description # eQuilibrator - a thermodynamics calculator for biochemical reactions [![PyPI version](https://badge.fury.io/py/equilibrator-api.svg)](https://badge.fury.io/py/equilibrator-api) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/equilibrator-api/badges/version.svg)](https://anaconda.org/conda-forge/equilibrator-api) [![pipeline status](https://gitlab.com/elad.noor/equilibrator-api/badges/master/pipeline.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![coverage report](https://gitlab.com/elad.noor/equilibrator-api/badges/master/coverage.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![Join the chat at https://gitter.im/equilibrator-devs/equilibrator-api](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Documentation Status](https://readthedocs.org/projects/equilibrator/badge/?version=latest)](https://equilibrator.readthedocs.io/en/latest/?badge=latest) ## 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). Note that the initialization might not work inside a Jupyter notebook environment - in that case you should try running it in a standard python shell first and then run the Jupyter notebook. ```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)}") ``` %package -n python3-equilibrator-api Summary: Calculation of standard thermodynamic potentials of biochemical reactions. Provides: python-equilibrator-api BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-equilibrator-api # eQuilibrator - a thermodynamics calculator for biochemical reactions [![PyPI version](https://badge.fury.io/py/equilibrator-api.svg)](https://badge.fury.io/py/equilibrator-api) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/equilibrator-api/badges/version.svg)](https://anaconda.org/conda-forge/equilibrator-api) [![pipeline status](https://gitlab.com/elad.noor/equilibrator-api/badges/master/pipeline.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![coverage report](https://gitlab.com/elad.noor/equilibrator-api/badges/master/coverage.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![Join the chat at https://gitter.im/equilibrator-devs/equilibrator-api](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Documentation Status](https://readthedocs.org/projects/equilibrator/badge/?version=latest)](https://equilibrator.readthedocs.io/en/latest/?badge=latest) ## 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). Note that the initialization might not work inside a Jupyter notebook environment - in that case you should try running it in a standard python shell first and then run the Jupyter notebook. ```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)}") ``` %package help Summary: Development documents and examples for equilibrator-api Provides: python3-equilibrator-api-doc %description help # eQuilibrator - a thermodynamics calculator for biochemical reactions [![PyPI version](https://badge.fury.io/py/equilibrator-api.svg)](https://badge.fury.io/py/equilibrator-api) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/equilibrator-api/badges/version.svg)](https://anaconda.org/conda-forge/equilibrator-api) [![pipeline status](https://gitlab.com/elad.noor/equilibrator-api/badges/master/pipeline.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![coverage report](https://gitlab.com/elad.noor/equilibrator-api/badges/master/coverage.svg)](https://gitlab.com/elad.noor/equilibrator-api/commits/master) [![Join the chat at https://gitter.im/equilibrator-devs/equilibrator-api](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Documentation Status](https://readthedocs.org/projects/equilibrator/badge/?version=latest)](https://equilibrator.readthedocs.io/en/latest/?badge=latest) ## 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). Note that the initialization might not work inside a Jupyter notebook environment - in that case you should try running it in a standard python shell first and then run the Jupyter notebook. ```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)}") ``` %prep %autosetup -n equilibrator-api-0.4.7 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-equilibrator-api -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Thu Jun 08 2023 Python_Bot - 0.4.7-1 - Package Spec generated