Metadata-Version: 1.1
Name: mbuild
Version: 0.4.2
Summary: mbuild is a component based molecule builder tool to assemble large molecular systems from reusable parts for molecular dynamics simulations
Home-page: https://github.com/sallai/mbuild
Author: Janos Sallai, Christoph Klein
Author-email: janos.sallai@vanderbilt.edu, christoph.klein@vanderbilt.edu
License: LGPL
Download-URL: https://github.com/sallai/mbuild/tarball/0.4.1
Description: mBuild: a hierarchical, component based molecule builder
        ========================================================
        
        .. image:: https://badge.fury.io/py/mbuild.png
            :target: http://badge.fury.io/py/mbuild
            
        .. image:: https://travis-ci.org/sallai/mbuild.png?branch=develop
                :target: https://travis-ci.org/sallai/mbuild
                
        .. image:: https://coveralls.io/repos/sallai/mbuild/badge.png?branch=develop 
                :target: https://coveralls.io/r/sallai/mbuild?branch=develop
        
        .. image:: https://readthedocs.org/projects/mbuild/badge/?version=develop
                :target: http://mbuild.readthedocs.org/en/develop/
                :alt: Documentation Status
        
        mBuild is a component based molecule builder tool used to assemble complex
        molecular systems from reusable parts for molecular dynamics simulations.
        
        * Documentation: http://mbuild.rtfd.org/en/master/
        
        ============
        Installation
        ============
        
        Install with pip
        ----------------
        
         $ pip install mbuild
        
        Dependencies
        ------------
        To use mbuild, the following libraries and software will need to be installed.
        
            Linux, Mac OS X or Windows operating system
                We develop mainly on 64-bit Mac and Windows machines. TravisCI is
                currently only set up to perform testing on Debian.
        
            `Python <http://python.org>`_ == 2.7
                 Once our unit tests flesh out a bit more, we intend to add support
                 for >=2.6.
        
            `NumPy <http://numpy.scipy.org/>`_ >= 1.6.0
                Numpy is the base package for numerical computing in python.
        
            `MDTraj <http://mdtraj.org/>`_ >=1.0.0
                MDTraj is a Python library for reading, writing and analyizing
                molecular dynamics trajectories. mBuild uses MDTraj as an entry and
                exit point for molecule data.
        
        Optional packages:
        
            `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_
                VMD (Visual Molecular Dynamics) is a visualization program. Currently,
                we only use a (very) thin wrapper to call it from the command-line
                when you want to look at a Compound that you've built. A more robust
                integration with partial control from Python is planned in the near
                future (see issue [#32](/../../issues/32)).
        
        To make your life easier, we recommend that you use a pre-packaged Python
        distribution like `Enthought's Canopy <https://www.enthought.com/products/canopy/>`_
        or `Continuum's Anaconda <https://store.continuum.io/>`_ in order to get all
        of the dependencies.
        
        =========================
        Testing your installation
        =========================
        
        mBuild uses `py.test` for unit testing. To run them simply type run the
        following while in the base directory:
        
         $ py.test
        
        We need a LOT more tests so any help here is especially welcome!
        
        ============
        Contributing
        ============
        
        Contributions are welcome, and they are greatly appreciated! Every
        little bit helps, and credit will always be given. 
        
        You can contribute in many ways:
        
        Types of Contributions
        ----------------------
        
        Report Bugs
        ~~~~~~~~~~~
        
        Report bugs at https://github.com/sallai/mbuild/issues.
        
        If you are reporting a bug, please include:
        
        * Your operating system name and version.
        * Any details about your local setup that might be helpful in troubleshooting.
        * Detailed steps to reproduce the bug.
        
        Fix Bugs
        ~~~~~~~~
        
        Look through the GitHub issues for bugs. Anything tagged with "bug"
        is open to whoever wants to implement it.
        
        Implement Features
        ~~~~~~~~~~~~~~~~~~
        
        Look through the GitHub issues for features. Anything tagged with "enhancement"
        is open to whoever wants to implement it.
        
        Write Documentation
        ~~~~~~~~~~~~~~~~~~~
        
        mbuild could always use more documentation, whether as part of the 
        official mbuild docs, in docstrings, or even on the web in blog posts,
        articles, and such.
        
        Submit Feedback
        ~~~~~~~~~~~~~~~
        
        The best way to send feedback is to file an issue at https://github.com/sallai/mbuild/issues.
        
        If you are proposing a feature:
        
        * Explain in detail how it would work.
        * Keep the scope as narrow as possible, to make it easier to implement.
        * Remember that this is a volunteer-driven project, and that contributions
          are welcome :)
        
        Get Started!
        ------------
        
        Ready to contribute? Here's how to set up `mbuild` for local development.
        
        1. Fork the `mbuild` repo on GitHub.
        2. Clone your fork locally::
        
            $ git clone git@github.com:your_name_here/mbuild.git
        
        3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
        
            $ mkvirtualenv mbuild
            $ cd mbuild/
            $ python setup.py develop
        
        4. Create a branch for local development::
        
            $ git checkout -b name-of-your-bugfix-or-feature
           
           Now you can make your changes locally.
        
        5. When you're done making changes, check that your changes pass flake8 and the tests::
        
            $ flake8 mbuild tests
            $ python setup.py test
        
           To get flake8, just pip install it into your virtualenv.
        
        6. Commit your changes and push your branch to GitHub::
        
            $ git add .
            $ git commit -m "Your detailed description of your changes."
            $ git push origin name-of-your-bugfix-or-feature
        
        7. Submit a pull request through the GitHub website.
        
        Pull Request Guidelines
        -----------------------
        
        Before you submit a pull request, check that it meets these guidelines:
        
        1. The pull request should include tests.
        2. If the pull request adds functionality, the docs should be updated. Put
           your new functionality into a function with a docstring.
        3. The pull request should work for Python 2.7 (we intend to provide support for 2.6 and 3.3+ in the near future). Check 
           https://travis-ci.org/sallai/mbuild/pull_requests
           and make sure that the tests pass for all supported Python versions.
        
        
        
        
        
        History
        -------
        
        0.4.0 (2014-10-14)
        ++++++++++++++++++
        
        * First release on PyPI.
        
Keywords: mbuild
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
