Copyright for mdtraj source package in Jammy

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: mdtraj
Upstream-Contact: Robert McGibbon
Source: https://github.com/mdtraj/mdtraj

Files: *
Copyright: 2012-2020 Robert McGibbon and contributers
License: LGPL-2.1+

Files: mdtraj/utils/six.py
Copyright: 2010-2013 Benjamin Peterson
License: Expat

Files: mdtraj/utils/unit/*
Copyright: 2012 Christopher M. Bruns and Peter Eastman
 with Stanford University
License: Expat
Comments:
 From simtk. This is part of the OpenMM molecular simulation toolkit
 originating from Simbios, the NIH National Center for Physics-Based
 Simulation of Biological Structures at Stanford, funded under the NIH
 Roadmap for Medical Research, grant U54 GM072970.
 See https://simtk.org.

Files: mdtraj/core/topology.py
Copyright: 2012-2014 Peter Eastman, Robert McGibbon
 Kyle A. Beauchamp, Matthew Harrigan, Carlos Xavier Hernandez
 with Stanford University
License: LGPL-2.1+/Expat

Files: mdtraj/formats/gro.py
Copyright: 2012-2015 Robert McGibbon, Lee-Ping Wang, Peter Eastman,
 Jason Swails with Stanford University
License: LGPL-2.1+/Expat

Files: mdtraj/formats/mol2.py
Copyright: 2012-2013 Kyle A. Beauchamp,
 Robert McGibbon, John D. Chodera
 with Stanford University
License: LGPL-2.1+/Expat

Files: mdtraj/formats/prmtop.py
Copyright: 2012-2013 TJ Lane,
 Robert McGibbon, Jason Swails
 with Stanford University and Peter Eastman
License: LGPL-2.1+/Expat

Files: mdtraj/formats/pdb/*
Copyright: 2012-2014 Peter Eastman, Robert McGibbon,
 Carlos Hernandez, Jason Swails
 with Stanford University
License: LGPL-2.1+/Expat

Files: mdtraj/formats/binpos/src/*  mdtraj/formats/binpos/include/*
 mdtraj/formats/dcd/src/* mdtraj/formats/dcd/include/*
 mdtraj/formats/dtr/include/*.h
Copyright: 1995-2009 The Board of Trustees of the University of Illinois
License: LGPL-2.1+

Files: mdtraj/formats/tng/src/compression/*
 mdtraj/formats/tng/include/compression/*
 mdtraj/formats/tng/src/lib/tng_io.c
 mdtraj/formats/tng/include/tng/*.h
Copyright: 2010-2014 Daniel Spangberg, Magnus Lundborg
 and the GROMACS development team
License: Revised-BSD

Files: mdtraj/formats/tng/include/tng/tng_io.hpp
Copyright: 2012-2013 Anders Gärdenäs
 and the GROMACS development team
License: Revised-BSD

Files: mdtraj/formats/tng/src/lib/md5.c
 mdtraj/formats/tng/include/tng/md5.h
Copyright: 1999, 2000, 2002 L. Peter Deutsch, Aladdin Enterprises
License: Revised-BSD

Files: mdtraj/formats/dtr/src/* mdtraj/formats/dtr/include/dtrplugin.hxx
Copyright: 2009, D. E. Shaw Research, LLC
License: BSD-3-Clause

Files: mdtraj/formats/xtc/src/*
 mdtraj/formats/xtc/include/*
Copyright: 2009-2014, Erik Lindahl & David van der Spoel,
 Robert T. McGibbon
License: BSD-2-Clause
 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.
Comment:
 Adapted from xdrfile-1.1.4
 http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
 ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz

Files: mdtraj/formats/xtc/include/ms_stdint.h
Copyright: 2006-2013 Alexander Chemeris
License: BSD-3-Clause

Files: mdtraj/rmsd/src/Munkres.cpp
 mdtraj/rmsd/include/Munkres.h
Copyright: 2012, Jacob Frelinger
License: BSD-2-Simple
 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.
 .
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING

Files: mdtraj/rmsd/include/sse_swizzle.h
Copyright: 2011 Imran Haque 
License: MIT
 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.

Files: mdtraj/testing/docscrape.py
Copyright: 2005-2011, NumPy Developers
License: BSD-3-Clause
Comment:
 This code is copied directly from numpy
 numpy / doc / sphinxext / docscrape.py

Files: debian/*
Copyright: 2020 Drew Parsons 
License: LGPL-2.1+

License: LGPL-2.1+
 MDTraj is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as
 published by the Free Software Foundation, either version 2.1
 of the License, or (at your option) any later version.
 .
 This library 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 Lesser General Public License for more details.
 .
 You should have received a copy of the GNU Lesser General Public
 License along with MDTraj. If not, see .
 .
 On Debian systems the full license text can be found at
 /usr/share/common-licenses/LGPL-2.1

License: Expat
 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.

License: Revised-BSD
 This software is provided 'as-is', without any express or implied
 warranty.  In no event will the authors be held liable for any
 damages arising from the use of this software.
 .
 Permission is granted to anyone to use this software for any purpose,
 including commercial applications, and to alter it and redistribute
 it freely, subject to the following restrictions:
 .
 1. The origin of this software must not be misrepresented; you must not
    claim that you wrote the original software. If you use this software
    in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
 .
 2. Altered source versions must be plainly marked as such, and must not be
    misrepresented as being the original software.
 .
 3. This notice may not be removed or altered from any source distribution.

License: BSD-3-Clause
 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 product 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
 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.

License: LGPL-2.1+/Expat
 Released under the terms of LGPL-2.1+, the GNU Lesser General Public
 License, version 2.1 of the License, or (at your option) any later
 version.
 .
 Portions of this code originate from the OpenMM molecular simulation
 toolkit, copyright (c) 2012 Stanford University and Peter Eastman. Those
 portions are distributed under the Expat License.