Metadata-Version: 2.1
Name: MDAnalysis
Version: 1.0.0
Summary: An object-oriented toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.
Home-page: https://www.mdanalysis.org
Author: Naveen Michaud-Agrawal
Author-email: naveen.michaudagrawal@gmail.com
Maintainer: Richard Gowers
Maintainer-email: mdnalysis-discussion@googlegroups.com
License: GPL 2
Download-URL: https://github.com/MDAnalysis/mdanalysis/releases
Project-URL: Documentation, https://www.mdanalysis.org/docs/
Project-URL: Issue Tracker, https://github.com/mdanalysis/mdanalysis/issues
Project-URL: User Group, https://groups.google.com/forum/#!forum/mdnalysis-discussion
Project-URL: Source, https://github.com/mdanalysis/mdanalysis
Description: .. Summary for PyPI
        .. https://pypi.python.org/project/MDAnalysis/
        
        |build| |cov| |docs| |usergroup| |developergroup| |anaconda| |mybinder|
        
           
        MDAnalysis_ is an object-oriented python toolkit to analyze molecular
        dynamics trajectories generated by CHARMM_, Gromacs_, Amber_, NAMD_,
        or LAMMPS_; it also reads other formats (e.g. PDB_ files and `XYZ
        format`_ trajectories; see the `Table of Supported Coordinate
        Formats`_ and `Table of Supported Topology Formats`_ for details). It
        can write most of the coordinate formats, too, together with atom
        selections for use in Gromacs_, CHARMM_, VMD_ and PyMOL_ (see
        `Selection exporters`_).
        
        MDAnalysis allows one to read molecular dynamics trajectories and
        access the atomic coordinates through NumPy_ arrays. This provides a
        flexible and relatively fast framework for complex analysis tasks that
        integrates well with the wider Python ecosystem. Fairly complete `atom
        selection commands`_ are implemented. Trajectories can also be
        manipulated (for instance, fit to a reference structure) and written
        out in a range of formats.
        
        
        Availability
        ============
        
        **Source code** is available from https://www.mdanalysis.org under the `GNU
        Public Licence, version 2`_, together with the `online
        documentation`_. **Packages** can be downloaded from
        https://pypi.org/project/MDAnalysis/ or installed/upgraded via PyPI using `pip`_::
        
          pip install --upgrade MDAnalysis
        
        By default MDAnalysis does not install every dependency needed to run every
        analysis available in the analysis module or read netcdf Amber_ trajectories.
        To install and update these dependencies as well run ::
        
          pip install --upgrade 'MDAnalysis[analysis,AMBER]
        
        Please report **bugs** or **enhancement requests** through the `Issue
        Tracker`_. Questions can also be asked on the `mdnalysis-discussion mailing
        list`_.
        
        In order to run the `Unit Tests`_ it is also necessary to install a
        separate package MDAnalysisTests_ containing the test and test
        data. As it contains about 70 MB of molecular dynamics trajectories
        and simulation system structures it is not included with the library
        itself.
        
        
        Citation
        ========
        
        When using MDAnalysis in published work, please cite the following
        two papers:
        
        *   R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
            M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
            S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
            A Python package for the rapid analysis of molecular
            dynamics simulations. In S. Benthall and S. Rostrup,
            editors, Proceedings of the 15th Python in Science
            Conference, pages 102-109, Austin, TX, 2016. SciPy.
        
        *   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
            and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
            Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.
            doi:`10.1002/jcc.21787`_
        
        For citations of included algorithms and sub-modules please see the references_.
        
        
        .. Links
        
        .. _MDAnalysis: https://www.mdanalysis.org
        .. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787
        .. _references: https://docs.mdanalysis.org/documentation_pages/references.html
        .. _GNU Public Licence, version 2: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
        .. _Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues
        .. _`mdnalysis-discussion mailing list`:
           https://groups.google.com/group/mdnalysis-discussion
        .. _`online documentation`:
           https://docs.mdanalysis.org
        .. _`Table of Supported Coordinate Formats`:
           https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
        .. _`Table of Supported Topology Formats`:   
           https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
        .. _`atom selection commands`:
           https://docs.mdanalysis.org/documentation_pages/selections.html#selection-commands
        .. _`Selection exporters`:
           https://docs.mdanalysis.org/documentation_pages/selections_modules.html#selection-exporters
        .. _NumPy: https://numpy.scipy.org
        .. _CHARMM:  https://www.charmm.org/
        .. _Amber:   http://ambermd.org/
        .. _LAMMPS:  http://lammps.sandia.gov/
        .. _NAMD:    http://www.ks.uiuc.edu/Research/namd/
        .. _Gromacs: http://www.gromacs.org/
        .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
        .. _PyMOL: https://www.pymol.org/
        .. _PDB: https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
        .. _XYZ format: https://openbabel.org/wiki/XYZ_%28format%29
        
        .. _Unit Tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
        .. _MDAnalysisTests: https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests
        
        .. _`pip`: https://www.pip-installer.org/en/latest/index.html
        
        
        .. badges
        .. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
           :alt: User Google Group
           :target: http://users.mdanalysis.org
        
        .. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
           :alt: Developer Google Group
           :target: http://developers.mdanalysis.org
        
        .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
           :alt: Documentation (latest release)
           :target: https://docs.mdanalysis.org
        
        .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop
           :alt: Build Status
           :target: https://travis-ci.org/MDAnalysis/mdanalysis
        
        .. |cov|   image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg
           :alt: Coverage Status
           :target: https://codecov.io/gh/MDAnalysis/mdanalysis
        
        .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg
           :alt: Anaconda
           :target: https://anaconda.org/conda-forge/mdanalysis
        
        .. |mybinder| image:: https://mybinder.org/badge.svg
           :alt: My Binder
           :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master
           
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows 
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: C
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires: numpy (>=1.13.3)
Requires: biopython (>= 1.71)
Requires: mmtf (>=1.0.0)
Requires: networkx (>=1.0)
Requires: GridDataFormats (>=0.3.2)
Requires: joblib
Requires: scipy (>=1.0.0)
Requires: matplotlib (>=1.5.1)
Requires: tqdm (>=4.43.0)
Provides: MDAnalysis
Description-Content-Type: text/x-rst
Provides-Extra: AMBER
Provides-Extra: analysis
