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mdtraj: carry forward riscv64 patches to 1.11.2
Nightly version bump omitted the patches/mdtraj/<version> directory for 1.11.2, so the build's unconditional `git apply .../*.patch` step failed with "No such file or directory" before any build/test ran. Copied forward the same patch set from 1.11.1.post2 (unchanged since then).
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‎patches/mdtraj/1.11.2/0001-Ship-the-licences-of-the-third-party-code-compiled-in.patch‎

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From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
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From: Ludovic Henry <git@ludovic.dev>
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Date: Fri, 2 Oct 2026 12:00:00 +0200
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Subject: [PATCH] Ship the licences of the third-party code compiled into the
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extensions
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The wheel's extensions compile in code from five other projects under
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their own permissive licences, each of which requires its notice to
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travel with binary redistributions: the VMD molfile plugin library
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(University of Illinois Open Source License; mdtraj.formats.dcd and the
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plugin headers of mdtraj.formats.dtr), D. E. Shaw Research's dtrplugin
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(BSD-3-Clause; mdtraj.formats.dtr), the xdrfile library (BSD-2-Clause;
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mdtraj.formats.xtc and .trr), Jacob Frelinger's Munkres implementation
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(BSD; mdtraj._lprmsd) and OpenMM's vectorization headers (MIT; the
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mdtraj.geometry extensions). The notices only live in the source file
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headers, so every published wheel carries mdtraj's own LGPL LICENSE alone.
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Add one LICENSE.<component> file per component at the project root,
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reproducing the notice its sources carry (the VMD sources only carry the
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copyright line, so the UIUC Open Source License text is taken from the
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VMD plugin library's licence page). setuptools' default license_files
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glob already matches LICENSE.* at the root, so no setup.py change is
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needed and the files land in dist-info/licenses/.
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Upstream-Status: To upstream [not submitted from this automated port run; needs a pull request against mdtraj/mdtraj]
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---
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LICENSE.dtrplugin | 32 ++++++++++++++++++++++++++++++++
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LICENSE.munkres | 13 +++++++++++++
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LICENSE.openmm | 32 ++++++++++++++++++++++++++++++++
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LICENSE.vmd-plugins | 45 +++++++++++++++++++++++++++++++++++++++++++++
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LICENSE.xdrfile | 26 ++++++++++++++++++++++++++
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5 files changed, 148 insertions(+)
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create mode 100644 LICENSE.dtrplugin
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create mode 100644 LICENSE.munkres
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create mode 100644 LICENSE.openmm
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create mode 100644 LICENSE.vmd-plugins
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create mode 100644 LICENSE.xdrfile
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diff --git a/LICENSE.dtrplugin b/LICENSE.dtrplugin
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new file mode 100644
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index 0000000..b097e44
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--- /dev/null
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+++ b/LICENSE.dtrplugin
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+The D. E. Shaw Research dtrplugin compiled into mdtraj.formats.dtr
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+(mdtraj/formats/dtr/src/dtrplugin.cxx) carries the following notice:
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+
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+Copyright 2009, D. E. Shaw Research, LLC
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+All rights reserved.
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+
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+Redistribution and use in source and binary forms, with or without
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+modification, are permitted provided that the following conditions are
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+met:
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+
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+* Redistributions of source code must retain the above copyright
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+ notice, this list of conditions, and the following disclaimer.
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+
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+* Redistributions in binary form must reproduce the above copyright
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+ notice, this list of conditions, and the following disclaimer in the
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+ documentation and/or other materials provided with the distribution.
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+
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+* Neither the name of D. E. Shaw Research, LLC nor the names of its
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+ contributors may be used to endorse or promote products derived from
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+ this software without specific prior written permission.
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+
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+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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diff --git a/LICENSE.munkres b/LICENSE.munkres
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new file mode 100644
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index 0000000..338c6b7
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--- /dev/null
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+++ b/LICENSE.munkres
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+The Munkres (Hungarian algorithm) implementation compiled into mdtraj._lprmsd
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+(mdtraj/rmsd/src/Munkres.cpp, from https://github.com/jfrelinger/cython-munkres-wrapper)
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+carries the following notice, reproduced as it appears in the source:
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+
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+Copyright (c) 2012, Jacob Frelinger
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+All rights reserved.
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+
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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:
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+
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+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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+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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+
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+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
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diff --git a/LICENSE.openmm b/LICENSE.openmm
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new file mode 100644
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index 0000000..7604496
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--- /dev/null
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+++ b/LICENSE.openmm
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+The vectorization headers compiled into the mdtraj.geometry extensions
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+(mdtraj/geometry/include/vectorize*.h) are taken from OpenMM and carry the
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+following notice:
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+
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+OpenMM
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+--------------------------------------------------------------------------
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+This is part of the OpenMM molecular simulation toolkit originating from
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+Simbios, the NIH National Center for Physics-Based Simulation of
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+Biological Structures at Stanford, funded under the NIH Roadmap for
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+Medical Research, grant U54 GM072970. See https://simtk.org.
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+
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+Portions copyright (c) 2014-2018 Stanford University and the Authors.
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+Authors: Peter Eastman
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+Contributors:
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+
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+Permission is hereby granted, free of charge, to any person obtaining a
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+copy of this software and associated documentation files (the "Software"),
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+to deal in the Software without restriction, including without limitation
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+the rights to use, copy, modify, merge, publish, distribute, sublicense,
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+and/or sell copies of the Software, and to permit persons to whom the
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+Software is furnished to do so, subject to the following conditions:
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+
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+The above copyright notice and this permission notice shall be included in
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+all copies or substantial portions of the Software.
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+
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+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
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+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
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+USE OR OTHER DEALINGS IN THE SOFTWARE.
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diff --git a/LICENSE.vmd-plugins b/LICENSE.vmd-plugins
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new file mode 100644
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index 0000000..c669ca3
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--- /dev/null
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+++ b/LICENSE.vmd-plugins
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@@ -0,0 +1,45 @@
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+The DCD reader/writer (mdtraj/formats/dcd) and the molfile plugin headers
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+used by mdtraj/formats/dcd and mdtraj/formats/dtr are taken from the VMD
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+plugin library and carry the following notice:
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+
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+(C) Copyright 1995-2016 The Board of Trustees of the
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+ University of Illinois
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+ All Rights Reserved
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+
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+The VMD plugin library is distributed under the University of Illinois
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+Open Source License (https://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html):
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+
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+University of Illinois Open Source License
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+Copyright 2006 Theoretical and Computational Biophysics Group,
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+All rights reserved.
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+
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+Developed by: Theoretical and Computational Biophysics Group
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+ University of Illinois at Urbana-Champaign
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+ http://www.ks.uiuc.edu/
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+
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+Permission is hereby granted, free of charge, to any person obtaining a copy of
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+this software and associated documentation files (the Software), to deal with
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+the Software without restriction, including without limitation the rights to
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+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
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+of the Software, and to permit persons to whom the Software is furnished to
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+do so, subject to the following conditions:
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+
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+Redistributions of source code must retain the above copyright notice,
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+this list of conditions and the following disclaimers.
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+
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+Redistributions in binary form must reproduce the above copyright notice,
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+this list of conditions and the following disclaimers in the documentation
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+and/or other materials provided with the distribution.
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+
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+Neither the names of Theoretical and Computational Biophysics Group,
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+University of Illinois at Urbana-Champaign, nor the names of its contributors
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+may be used to endorse or promote products derived from this Software without
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+specific prior written permission.
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+
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+THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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+THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
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+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
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+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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+OTHER DEALINGS WITH THE SOFTWARE.
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diff --git a/LICENSE.xdrfile b/LICENSE.xdrfile
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new file mode 100644
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index 0000000..0d0c4a9
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--- /dev/null
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+++ b/LICENSE.xdrfile
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@@ -0,0 +1,26 @@
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+The xdrfile library compiled into mdtraj.formats.xtc and mdtraj.formats.trr
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+(mdtraj/formats/xtc/src/xdrfile*.c) carries the following notice:
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+
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+Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
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+All rights reserved.
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+
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+Redistribution and use in source and binary forms, with or without
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+modification, are permitted provided that the following conditions are met:
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+
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+1. Redistributions of source code must retain the above copyright notice, this
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+list of conditions and the following disclaimer.
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+
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+2. Redistributions in binary form must reproduce the above copyright notice,
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+this list of conditions and the following disclaimer in the documentation
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+and/or other materials provided with the distribution.
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+
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+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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