MDAnalysis

Name	MDAnalysis JSON
Version	2.7.0 JSON
	download
home_page	https://www.mdanalysis.org
Summary	An object-oriented toolkit to analyze molecular dynamics trajectories.
upload_time	2023-12-27 00:28:48
maintainer	MDAnalysis Core Developers
docs_url	None
author	MDAnalysis Development Team
requires_python	>=3.9
license	========================================================================== Licenses of components of MDAnalysis ========================================================================== GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. 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To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". 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You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. <signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. ========================================================================== 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 - lib/formats/include/xdrfile_xtc.h - lib/formats/include/xdrfile_trr.h Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ========================================================================== CatDCD is released under the UIUC Open Source License: http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html University of Illinois Open Source License 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/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. Neither the names of Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. ========================================================================== Biopython License Agreement Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE ========================================================================== 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. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holders nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ========================================================================== 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: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (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 Creative Commons Attribution-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. The logo is contained in the file 'mdanalysis-logo.png'. Derivatives in the files 'mdanalysis-logo-127x55.png', 'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for inclusion in MDAnalysis and on websites related to MDAnalysis. They are distributed under the same license as the 'Atom' logo. ==========================================================================
keywords	python science chemistry biophysics molecular-dynamics computational-chemistry molecular-simulation analysis trajectory-analysis
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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 letting 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 packaged under the
GNU General Public License, version 3 or any later version. Invidiual
source code components are provided under a mixture of GPLv3+ compatible
licenses, including LGPLv2.1+ and GPLv2+. Please see the file LICENSE_
for more information.


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

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

If you are a **new developer** who would like to start contributing to
MDAnalysis get in touch on `GitHub Discussions`_. 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/develop/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
.. _`GitHub Discussions`:
   https://github.com/MDAnalysis/mdanalysis/discussions
.. _`developer guide`:
   https://userguide.mdanalysis.org/contributing.html
.. _`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

.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
   :alt: Documentation (latest release)
   :target: https://docs.mdanalysis.org

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

.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
   :alt: Powered by NumFOCUS
   :target: https://www.numfocus.org/

.. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg
   :alt: Github Actions Build Status
   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml

.. |cron| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml/badge.svg
   :alt: Github Actions Cron Job Status
   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml

.. |cirruscron| image:: https://img.shields.io/cirrus/github/MDAnalysis/mdanalysis/develop
   :alt: Cirrus CI - Cron job status
   :target: https://cirrus-ci.com/github/MDAnalysis/mdanalysis/develop

.. |linters| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml/badge.svg
   :alt: Github Actions Linters Status
   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml

.. |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
   
.. |asv| image:: https://img.shields.io/badge/benchmarked%20by-asv-blue.svg
   :alt: ASV Benchmarks
   :target:  https://www.mdanalysis.org/benchmarks/

.. |powered_by_MDA| image:: https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=15&logo=data:image/x-icon;base64,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
   :alt: Powered by MDAnalysis
   :target: https://www.mdanalysis.org

.. |discussions| image:: https://img.shields.io/github/discussions/MDAnalysis/MDAnalysis
   :alt: GitHub Discussions
   :target: https://github.com/MDAnalysis/mdanalysis/discussions

            

Raw data

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    "_id": null,
    "home_page": "https://www.mdanalysis.org",
    "name": "MDAnalysis",
    "maintainer": "MDAnalysis Core Developers",
    "docs_url": null,
    "requires_python": ">=3.9",
    "maintainer_email": "MDAnalysis Core Developers <mdanalysis@numfocus.org>",
    "keywords": "python,science,chemistry,biophysics,molecular-dynamics,computational-chemistry,molecular-simulation,analysis,trajectory-analysis",
    "author": "MDAnalysis Development Team",
    "author_email": "MDAnalysis Development Team <mdanalysis@numfocus.org>",
    "download_url": "https://files.pythonhosted.org/packages/3e/67/c4ec984d4648c2435717fe8f35c54f22d6375eb0383060f8ebc21587bd13/MDAnalysis-2.7.0.tar.gz",
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    "description": "\n|numfocus| \n\n|build| |cron| |cirruscron| |linters| |cov|\n\n|docs| |devdocs| |discussions|\n\n|anaconda| |asv|\n\nMDAnalysis_ 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. \n\nIt works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others \u2014 see the lists of supported `trajectory formats`_ and `topology formats`_.\nMDAnalysis also includes widely used analysis algorithms in the `MDAnalysis.analysis`_ module.\n\n.. _numfocus-fiscal-sponsor-attribution:\n\nThe MDAnalysis project uses an `open governance model`_ and is fiscally sponsored by `NumFOCUS`_. Consider making \na `tax-deductible donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png\n   :alt: NumFOCUS (Fiscally Sponsored Project)\n   :target: https://numfocus.org/project/mdanalysis\n   :align: center\n\nThis project is bound by a `Code of Conduct`_.\n\n|powered_by_MDA|\n\nIf you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.\n\nExample analysis script\n=======================\n\n.. code:: python\n\n   import MDAnalysis as mda\n\n   # Load simulation results with a single line\n   u = mda.Universe('topol.tpr','traj.trr')\n\n   # Select atoms\n   ag = u.select_atoms('name OH')\n\n   # Atom data made available as Numpy arrays\n   ag.positions\n   ag.velocities\n   ag.forces\n\n   # Iterate through trajectories\n   for ts in u.trajectory:\n       print(ag.center_of_mass())\n\n\nDocumentation\n=============\n\n**New users** should read the `Quickstart Guide`_ and might want to\nlook at our videos_, in which core developers explain various aspects\nof MDAnalysis.\n\n**All users** should read the `User Guide`_.\n\n**Developers** may also want to refer to the `MDAnalysis API docs`_.\n\nA growing number of `tutorials`_ are available that explain how to\nconduct RMSD calculations, structural alignment, distance and contact\nanalysis, and many more.\n\n\nInstallation and availability\n=============================\n\nThe latest release can be **installed via pip or conda** as\ndescribed in the `Installation Quick Start`_.\n\n**Source code** is hosted in a git repository at\nhttps://github.com/MDAnalysis/mdanalysis and is packaged under the\nGNU General Public License, version 3 or any later version. Invidiual\nsource code components are provided under a mixture of GPLv3+ compatible\nlicenses, including LGPLv2.1+ and GPLv2+. Please see the file LICENSE_\nfor more information.\n\n\nContributing\n============\n\nPlease report **bugs** or **enhancement requests** through the `Issue\nTracker`_. Questions can also be asked on `GitHub Discussions`_.\n\nIf you are a **new developer** who would like to start contributing to\nMDAnalysis get in touch on `GitHub Discussions`_. To set up a\ndevelopment environment and run the test suite read the `developer\nguide`_.\n\n\nCitation\n========\n\nWhen using MDAnalysis in published work, please cite the following\ntwo papers:\n\n*   R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,\n    M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,\n    S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:\n    A Python package for the rapid analysis of molecular\n    dynamics simulations. In S. Benthall and S. Rostrup,\n    editors, Proceedings of the 15th Python in Science\n    Conference, pages 102-109, Austin, TX, 2016. SciPy.\n    doi:`10.25080/Majora-629e541a-00e`_    \n\n*   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,\n    and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular\n    Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.\n    doi:`10.1002/jcc.21787`_\n\nFor citations of included algorithms and sub-modules please see the references_.\n\n\n.. _NumFOCUS: https://numfocus.org/\n.. _open governance model: https://www.mdanalysis.org/about/#governance\n.. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis\n.. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/\n.. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats\n.. _MDAnalysis: https://www.mdanalysis.org\n.. _LICENSE:\n   https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE\n.. _`Installation Quick Start`:\n   https://www.mdanalysis.org/pages/installation_quick_start/\n.. _`MDAnalysis.analysis`: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html\n.. _`tutorials`: https://userguide.mdanalysis.org/examples/README.html\n.. _`videos`: https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos\n.. _`Quickstart Guide`:\n   https://userguide.mdanalysis.org/examples/quickstart.html\n.. _`User Guide`: https://userguide.mdanalysis.org\n.. _`MDAnalysis API docs`:\n   https://docs.mdanalysis.org\n.. _`Issue Tracker`: https://github.com/mdanalysis/mdanalysis/issues\n.. _`GitHub Discussions`:\n   https://github.com/MDAnalysis/mdanalysis/discussions\n.. _`developer guide`:\n   https://userguide.mdanalysis.org/contributing.html\n.. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787\n.. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e\n.. _references: https://docs.mdanalysis.org/documentation_pages/references.html\n.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis\n\n.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg\n   :alt: Documentation (latest release)\n   :target: https://docs.mdanalysis.org\n\n.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg\n   :alt: Documentation (development version)\n   :target: https://docs.mdanalysis.org/dev\n\n.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A\n   :alt: Powered by NumFOCUS\n   :target: https://www.numfocus.org/\n\n.. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg\n   :alt: Github Actions Build Status\n   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml\n\n.. |cron| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml/badge.svg\n   :alt: Github Actions Cron Job Status\n   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml\n\n.. |cirruscron| image:: https://img.shields.io/cirrus/github/MDAnalysis/mdanalysis/develop\n   :alt: Cirrus CI - 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    "license": "========================================================================== Licenses of components of MDAnalysis ==========================================================================   GNU GENERAL PUBLIC LICENSE Version 2, June 1991  Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.  Preamble  The licenses for most software are designed to take away your freedom to share and change it.  By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users.  This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it.  (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.)  You can apply it to your programs, too.  When we speak of free software, we are referring to freedom, not price.  Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.  To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.  For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have.  You must make sure that they, too, receive or can get the source code.  And you must show them these terms so they know their rights.  We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.  Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software.  If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.  Finally, any free program is threatened constantly by software patents.  We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary.  To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all.  The precise terms and conditions for copying, distribution and modification follow.  GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION  0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License.  The \"Program\", below, refers to any such program or work, and a \"work based on the Program\" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language.  (Hereinafter, translation is included without limitation in the term \"modification\".)  Each licensee is addressed as \"you\".  Activities other than copying, distribution and modification are not covered by this License; they are outside its scope.  The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.  1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.  You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.  2. 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(Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.)  These requirements apply to the modified work as a whole.  If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works.  But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.  Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.  In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.  3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:  a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,  b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,  c) Accompany it with the information you received as to the offer to distribute corresponding source code.  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These actions are prohibited by law if you do not accept this License.  Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.  6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions.  You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License.  7. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded.  In such case, this License incorporates the limitation as if written in the body of this License.  9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time.  Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.  Each version is given a distinguishing version number.  If the Program specifies a version number of this License which applies to it and \"any later version\", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation.  If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.  10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission.  For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this.  Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.  NO WARRANTY  11. 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It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the \"copyright\" line and a pointer to where the full notice is found.  <one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA   Also add information on how to contact you by electronic and paper mail.  If the program is interactive, make it output a short notice like this when it starts in an interactive mode:  Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.  The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License.  Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program.  You should also get your employer (if you work as a programmer) or your school, if any, to sign a \"copyright disclaimer\" for the program, if necessary.  Here is a sample; alter the names:  Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker.  <signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice  This General Public License does not permit incorporating your program into proprietary programs.  If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library.  If this is what you want to do, use the GNU Library General Public License instead of this License.   ==========================================================================  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 - lib/formats/include/xdrfile_xtc.h - lib/formats/include/xdrfile_trr.h  Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel All rights reserved.  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.  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Developed by:           Theoretical and Computational Biophysics Group University of Illinois at Urbana-Champaign http://www.ks.uiuc.edu/  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:  Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.  Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution.  Neither the names of Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission.  THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  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THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE   ==========================================================================  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.  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:  * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holders nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission.  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  ==========================================================================  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:  * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (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 Creative Commons Attribution-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.  The logo is contained in the file 'mdanalysis-logo.png'.  Derivatives in the files 'mdanalysis-logo-127x55.png', 'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for inclusion in MDAnalysis and on websites related to MDAnalysis. They are distributed under the same license as the 'Atom' logo.  ==========================================================================  ",
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