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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/unit/*
Copyright: 2012 Christopher M. Bruns and Peter Eastman
with Stanford University
License: Expat
Comment:
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/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/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 <ihaque@cs.stanford.edu>
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 <dparsons@debian.org>
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 <http://www.gnu.org/licenses/>.
.
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.
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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:
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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:
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* 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.
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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.
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