Metadata-Version: 2.1
Name: MDAnalysis
Version: 2.4.2
Summary: An object-oriented toolkit to analyze molecular dynamics trajectories.
Home-page: https://www.mdanalysis.org
Download-URL: https://github.com/MDAnalysis/mdanalysis/releases
Author: MDAnalysis Development Team
Author-email: MDAnalysis Development Team <mdanalysis@numfocus.org>
Maintainer: MDAnalysis Core Developers
Maintainer-email: MDAnalysis Core Developers <mdanalysis@numfocus.org>
License: ==========================================================================
        Licenses of components of MDAnalysis
        ==========================================================================
        
        
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        ==========================================================================
        
        Gromacs xdrfile library for reading XTC/TRR trajectories
          - lib/formats/src/xdrfile.c
          - lib/formats/src/xdrfile_xtc.c
          - lib/formats/src/xdrfile_trr.c
          - lib/formats/include/xdrfile.h
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        ==========================================================================
        
        CatDCD is released under the UIUC Open Source License:
        http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html
        
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        Copyright 2003-2007 Theoretical and Computational Biophysics Group,
        All rights reserved.
        
        Developed by:           Theoretical and Computational Biophysics Group
                                University of Illinois at Urbana-Champaign
                                http://www.ks.uiuc.edu/
        
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        ==========================================================================
        
                         Biopython License Agreement
        
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        ==========================================================================
        
        transformations module
          - transformations.py
          - transformations.c
        
        Copyright (c) 2006, Christoph Gohlke
        Copyright (c) 2006-2010, The Regents of the University of California
        All rights reserved.
        
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        ==========================================================================
        
        pyqcprot (src/pyqcprot) is released under the following 'BSD 3-clause' licence:
        
        -----------------------------------------------------------------------------
        PyQCPROT
        
            Author(s) of Original Implementation:     
                          Douglas L. Theobald
                          Department of Biochemistry
                          MS 009
                          Brandeis University
                          415 South St
                          Waltham, MA  02453
                          USA
        
                          dtheobald@brandeis.edu
                          
                          Pu Liu
                          Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
                          665 Stockton Drive
                          Exton, PA  19341
                          USA
        
                          pliu24@its.jnj.com
        
                          For the original code written in C see:
                          http://theobald.brandeis.edu/qcp/ 
        
        
            Author of Python Port:
                          Joshua L. Adelman
                          Department of Biological Sciences
                          University of Pittsburgh
                          Pittsburgh, PA 15260
                           
                          jla65@pitt.edu
        
         
            If you use this QCP rotation calculation method in a publication, please
            reference:
        
              Douglas L. Theobald (2005)
              "Rapid calculation of RMSD using a quaternion-based characteristic
              polynomial."
              Acta Crystallographica A 61(4):478-480.
        
              Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)
              "Fast determination of the optimal rotational matrix for macromolecular 
              superpositions."
              J. Comput. Chem. 31, 1561-1563. 
        
        
            Copyright (c) 2009-2010, Pu Liu and Douglas L. Theobald 
            Copyright (c) 2011       Joshua L. Adelman
            All rights reserved.
        
            Redistribution and use in source and binary forms, with or without modification, are permitted 
            provided that the following conditions are met:
        
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              of conditions and the following disclaimer in the documentation and/or other materials 
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            (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
            OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
        
        ==========================================================================
        
        MDAnalysis logo (see doc/sphinx/source/logos)
        
        The MDAnalysis 'Atom' logo was created by Christian Beckstein and is
        
        Copyright (c) 2011 Christian Beckstein
        
        MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a
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        Derivatives in the files 'mdanalysis-logo-127x55.png',
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        ==========================================================================
        
        
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Keywords: python,science,chemistry,biophysics,molecular-dynamics,computational-chemistry,molecular-simulation,analysis,trajectory-analysis
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|numfocus| |build| |cron| |travis| |cov|

|docs| |devdocs| |usergroup| |developergroup| |anaconda| |mybinder| |asv|

MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. 

It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported `trajectory formats`_ and `topology formats`_.
MDAnalysis also includes widely used analysis algorithms in the `MDAnalysis.analysis`_ module.

.. _numfocus-fiscal-sponsor-attribution:

The MDAnalysis project uses an `open governance model`_ and is fiscally sponsored by `NumFOCUS`_. Consider making 
a `tax-deductible donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png
   :alt: NumFOCUS (Fiscally Sponsored Project)
   :target: https://numfocus.org/project/mdanalysis
   :align: center

This project is bound by a `Code of Conduct`_.

|powered_by_MDA|

If you use MDAnalysis_ in your project consider lettting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.

Example analysis script
=======================

.. code:: python

   import MDAnalysis as mda

   # Load simulation results with a single line
   u = mda.Universe('topol.tpr','traj.trr')

   # Select atoms
   ag = u.select_atoms('name OH')

   # Atom data made available as Numpy arrays
   ag.positions
   ag.velocities
   ag.forces

   # Iterate through trajectories
   for ts in u.trajectory:
       print(ag.center_of_mass())


Documentation
=============

**New users** should read the `Quickstart Guide`_ and might want to
look at our videos_, in which core developers explain various aspects
of MDAnalysis.

**All users** should read the `User Guide`_.

**Developers** may also want to refer to the `MDAnalysis API docs`_.

A growing number of `tutorials`_ are available that explain how to
conduct RMSD calculations, structural alignment, distance and contact
analysis, and many more.


Installation and availability
=============================

The latest release can be **installed via pip or conda** as
described in the `Installation Quick Start`_.

**Source code** is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis and is available under the
GNU General Public License, version 2 (see the file LICENSE_).


Contributing
============

Please report **bugs** or **enhancement requests** through the `Issue
Tracker`_. Questions can also be asked on the `user mailing list`_.

If you are a **new developer** who would like to start contributing to
MDAnalysis get in touch on the `developer mailing list`_. To set up a
development environment and run the test suite read the `developer
guide`_.


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.
    doi:`10.25080/Majora-629e541a-00e`_    

*   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_.


.. _NumFOCUS: https://numfocus.org/
.. _open governance model: https://www.mdanalysis.org/about/#governance
.. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis
.. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/
.. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
.. _MDAnalysis: https://www.mdanalysis.org
.. _LICENSE:
   https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE
.. _`Installation Quick Start`:
   https://www.mdanalysis.org/pages/installation_quick_start/
.. _`MDAnalysis.analysis`: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html
.. _`tutorials`: https://userguide.mdanalysis.org/examples/README.html
.. _`videos`: https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos
.. _`Quickstart Guide`:
   https://userguide.mdanalysis.org/examples/quickstart.html
.. _`User Guide`: https://userguide.mdanalysis.org
.. _`MDAnalysis API docs`:
   https://docs.mdanalysis.org
.. _`Issue Tracker`: https://github.com/mdanalysis/mdanalysis/issues
.. _`user mailing list`:
   https://groups.google.com/group/mdnalysis-discussion
.. _`developer guide`:
   https://userguide.mdanalysis.org/contributing.html
.. _`developer mailing list`:
   https://groups.google.com/group/mdnalysis-devel
.. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787
.. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e
.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis


.. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
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.. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
   :alt: Developer Google Group
   :target: https://groups.google.com/group/mdnalysis-devel

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   :alt: Documentation (latest release)
   :target: https://docs.mdanalysis.org

.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg
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   :target: https://docs.mdanalysis.org/dev

.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
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   :alt: Github Actions Build Status
   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml

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   :alt: Github Actions Cron Job Status
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   :alt: Travis CI Build Status
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   :alt: ASV Benchmarks
   :target:  https://www.mdanalysis.org/benchmarks/

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