MDAnalysis

Name	MDAnalysis JSON
Version	2.8.0 JSON
	download
home_page	None
Summary	An object-oriented toolkit to analyze molecular dynamics trajectories.
upload_time	2024-11-22 21:18:24
maintainer	None
docs_url	None
author	None
requires_python	>=3.10
license	========================================================================== Licensing of the MDAnalysis library ========================================================================== The MDAnalyis library is packaged under the terms of the GNU Lesser General Public License version 3 or any later version (LGPLv3+). Developer contributions to the library are, unless otherwise stated, made under the GNU Lesser General Public License version 2.1 or any later version (LGPLv2.1+). The MDAnalysis library also includes external codes provided under licenses compatible with the terms of the GNU Lesser General Public License version 3 or any later version (LGPLv3+). These are outlined under "Licenses of components of MDAnalysis". ========================================================================== Licenses of components of MDAnalysis ========================================================================== GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 Copyright (C) 1991, 1999 Free Software Foundation, Inc. 51 Franklin Street, 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. [This is the first released version of the Lesser GPL. It also counts as the successor of the GNU Library Public License, version 2, hence the version number 2.1.] Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public Licenses are intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. 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Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: <program> Copyright (C) <year> <name of author> This program 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, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <https://www.gnu.org/licenses/>. The GNU 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 Lesser General Public License instead of this License. But first, please read <https://www.gnu.org/licenses/why-not-lgpl.html>. ========================================================================== 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. ========================================================================== DSSP module code for protein secondary structure assignment - analysis/dssp/pydssp_numpy.py MIT License Copyright (c) 2022 Shintaro Minami Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 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 AUTHORS 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 IN THE SOFTWARE. ========================================================================== 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
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage

            
|numfocus| 

|build| |cron| |cirruscron| |linters| |cov|

|docs| |devdocs| |discussions|

|anaconda| |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 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 Lesser General Public License, version 3 or any later version (LGPLv3+).
Invidiual source code components are provided under the
GNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+).
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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    "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 Lesser General Public License, version 3 or any later version (LGPLv3+).\nInvidiual source code components are provided under the\nGNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+).\nPlease see the file LICENSE_ for more information.\n\n\nContributing\n============\n\nPlease report **bugs** or **enhancement requests** through the `Issue\nTracker`_. 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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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The GNU 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 Lesser General Public License instead of this License.  But first, please read <https://www.gnu.org/licenses/why-not-lgpl.html>.  ==========================================================================  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. 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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.  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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.   ==========================================================================  DSSP module code for protein secondary structure assignment - analysis/dssp/pydssp_numpy.py  MIT License  Copyright (c) 2022 Shintaro Minami  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in 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:  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.  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 AUTHORS 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 IN THE SOFTWARE.  ==========================================================================  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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