.. _license:

License
===============================================================================

ProDy
-------------------------------------------------------------------------------

ProDy is available under the `MIT License`_::

  ProDy: A Python Package for Protein Dynamics Analysis

  Copyright (C) 2010-2014 University of Pittsburgh

  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.

.. _MIT License: http://opensource.org/licenses/MIT

Biopython
-------------------------------------------------------------------------------

`Biopython<https://biopython.org/>`_ KDTree package and TreeConstruction module are distributed with the ProDy
package.  Biopython is developed by The Biopython Consortium and is available
under the `Biopython license`_::

                   Biopython License Agreement

  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.

.. _Biopython license: http://www.biopython.org/DIST/LICENSE

Pyparsing
-------------------------------------------------------------------------------

The pyparsing_ module is distributed with the ProDy package.  Pyparsing is
developed by Paul T. McGuire and is available under the `MIT License`_::

  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.


Argparse
-------------------------------------------------------------------------------

The `argparse module <http://code.google.com/p/argparse/>`_ is distributed
with the ProDy package. Argparse is developed by Steven J. Bethard and
is available under the `Python Software Foundation License`_.

.. _Python Software Foundation License: http://docs.python.org/license.html

CEalign
-------------------------------------------------------------------------------

CEalign module is distributed with ProDy. The original CE method was developed 
by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy 
is developed by Jason Vertrees and available under the New BSD license::

  Copyright (c) 2007, Jason Vertrees.
  All rights reserved.

  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.


scikit-learn
-------------------------------------------------------------------------------
The discretization method for spectral clustering is redistributed and adapted 
with ProDy. scikit-learn is a Python module for machine learning built on top of 
SciPy and is distributed under the 3-Clause BSD license. The project was started 
in 2007 by David Cournapeau as a Google Summer of Code project, and since then 
many volunteers have contributed. 

  New BSD License

  Copyright (c) 2007–2019 The scikit-learn developers.
  All rights reserved.


  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are met:

    a. Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.
    b. 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.
    c. Neither the name of the Scikit-learn Developers  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 REGENTS 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.
  