Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/prody/ProDy
Upstream-Name: ProDy
Upstream-Contact: https://github.com/prody/ProDy/issues
Files-Excluded:
 *.bat
 docs/_static/css/basic.css
 docs/_static/css/bootswatch-united.min.css
 docs/_static/js/*.min.js
 docs/_static/js/doctools.js
 docs/_static/js/searchtools.js
 docs/_static/js/swfobject.js
 docs/_static/js/zeroclipboard.swf
 docs/_theme
 prody/proteins/hpbmodule/hpb_Python*
 scripts/*.bat

Files: *
Copyright: 2009-2014, University of Pittsburgh
License: Expat

Files: prody/dynamics/essa.py
 prody/dynamics/clustenm.py
Copyright: 2020, Burak Kaynak <burak.kaynak@pitt.edu> and Pemra Doruker <doruker@pitt.edu>
License: Expat

Files: prody/dynamics/editing.py
Copyright: 2009-2010, Joseph N. Stember and Willy Wriggers
License: permissive
 The authors hereby grant permission to use, copy, modify, and re-distribute this
 software and its documentation for any purpose, provided that existing copyright
 notices are retained in all copies and that this notice is included verbatim in
 any distributions. No written agreement, license, or royalty fee is required for
 any of the authorized uses.
 .
 IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT,
 INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE
 OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE
 AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 .
 THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING,
 BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
 PARTICULAR PURPOSE, AND NON-INFRINGEMENT.  THIS SOFTWARE IS PROVIDED ON AN "AS
 IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE
 MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

Files: prody/proteins/ccealign/*
Copyright: 2007, Jason Vertrees
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:
 .
  * 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, 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.

Files: prody/proteins/hpbmodule/*
Copyright: 2023, Xin Cao, Michelle H. Hummel, Bihua Yu, Evangelos A. Coutsias
License: Expat

Files: prody/utilities/TreeConstruction.py
Copyright: 2013, Yanbo Ye <yeyanbo289@gmail.com>
License: Biopython or BSD-3-Clause

Files: prody/utilities/tnt/*
Copyright: National Institute of Standards
License: public-domain
 This software was developed at the National Institute of Standards and
 Technology (NIST) by employees of the Federal Government in the course
 of their official duties. Pursuant to title 17 Section 105 of the
 United States Code, this software is not subject to copyright protection
 and is in the public domain. NIST assumes no responsibility whatsoever for
 its use by other parties, and makes no guarantees, expressed or implied,
 about its quality, reliability, or any other characteristic.

Files: debian/*
Copyright: 2022-2024, Andrius Merkys <merkys@debian.org>
License: Expat

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:
 .
  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.
  3. The name of the author may not be used to endorse or promote products
     derived from this software without specific prior written permission.
 .
 THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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: Biopython
 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
 OR PERFORMANCE OF THIS SOFTWARE.

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, 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 IN THE SOFTWARE.
