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 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. 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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.