Metadata-Version: 2.1
Name: wc_utils
Version: 0.0.19
Summary: Utilities for whole-cell modeling
Home-page: https://github.com/KarrLab/wc_utils
Author: Karr Lab
Author-email: info@karrlab.org
License: MIT
Download-URL: https://github.com/KarrLab/wc_utils
Description: |PyPI package| |Documentation| |Test results| |Test coverage| |Code
        analysis| |License| |Analytics|
        
        Whole-cell modeling utilities
        =============================
        
        This package contains utilities that are useful to multiple whole-cell
        (WC) software components.
        
        Installation
        ------------
        
        1. Install the third-party dependencies listed below. Detailed
           installation instructions are available in `An Introduction to
           Whole-Cell
           Modeling <http://docs.karrlab.org/intro_to_wc_modeling/master/0.0.1/installation.html>`__.
        
           -  `ChemAxon Marvin <https://chemaxon.com/products/marvin>`__:
              optional to calculate major protonation states
           -  `Java <https://www.java.com>`__ >= 1.8
           -  `Git <https://git-scm.com/>`__
           -  `OpenBabel <http://openbabel.org>`__: optional to calculate
              chemical formulae
           -  `Pip <https://pip.pypa.io>`__ >= 18.0
           -  `Python <https://www.python.org>`__ >= 3.6
        
        2. To use Marvin to calculate major protonation states, set
           ``JAVA_HOME`` to the path to your Java virtual machine (JVM)
           ``export JAVA_HOME=/usr/lib/jvm/default-java``
        
        3. To use Marvin to calculate major protonation states, add Marvin to
           the Java class path
           ``export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar``
        
        4. Install this package
        
           -  Install the latest release from PyPI ``pip install wc_utils[all]``
        
           -  Install the latest revision from GitHub
              ``pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils[all]   pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]``
        
        Example usage
        -------------
        
        Documentation
        -------------
        
        Please see the `API documentation <http://docs.karrlab.org/wc_utils>`__.
        
        License
        -------
        
        The build utilities are released under the `MIT license <LICENSE>`__.
        
        Development team
        ----------------
        
        This package was developed by the `Karr Lab <http://www.karrlab.org>`__
        at the Icahn School of Medicine at Mount Sinai in New York, USA.
        
        -  Arthur Goldberg
        -  Jonathan Karr
        
        Questions and comments
        ----------------------
        
        Please contact the `Karr Lab <http://www.karrlab.org>`__ with any
        questions or comments.
        
        .. |PyPI package| image:: https://img.shields.io/pypi/v/wc_utils.svg
           :target: https://pypi.python.org/pypi/wc_utils
        .. |Documentation| image:: https://readthedocs.org/projects/wc-utils/badge/?version=latest
           :target: http://docs.karrlab.org/wc_utils
        .. |Test results| image:: https://circleci.com/gh/KarrLab/wc_utils.svg?style=shield
           :target: https://circleci.com/gh/KarrLab/wc_utils
        .. |Test coverage| image:: https://coveralls.io/repos/github/KarrLab/wc_utils/badge.svg
           :target: https://coveralls.io/github/KarrLab/wc_utils
        .. |Code analysis| image:: https://api.codeclimate.com/v1/badges/8139298cdbc1e32dcde4/maintainability
           :target: https://codeclimate.com/github/KarrLab/wc_utils
        .. |License| image:: https://img.shields.io/github/license/KarrLab/wc_utils.svg
           :target: LICENSE
        .. |Analytics| image:: https://ga-beacon.appspot.com/UA-86759801-1/wc_utils/README.md?pixel
        
        
Keywords: whole-cell modeling
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Provides-Extra: chem
Provides-Extra: git
Provides-Extra: logging
Provides-Extra: quilt
Provides-Extra: protonation
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: all
