LICENSE

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Licenses of components of MDAnalysis
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		    GNU GENERAL PUBLIC LICENSE
		       Version 2, June 1991

 Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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==========================================================================

Gromacs xdrfile library for reading XTC/TRR trajectories
  - lib/formats/src/xdrfile.c
  - lib/formats/src/xdrfile_xtc.c
  - lib/formats/src/xdrfile_trr.c
  - lib/formats/include/xdrfile.h
  - lib/formats/include/xdrfile_xtc.h
  - lib/formats/include/xdrfile_trr.h

Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
All rights reserved.

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.

==========================================================================

CatDCD is released under the UIUC Open Source License:
http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html

University of Illinois Open Source License
Copyright 2003-2007 Theoretical and Computational Biophysics Group,
All rights reserved.

Developed by:           Theoretical and Computational Biophysics Group
                        University of Illinois at Urbana-Champaign
                        http://www.ks.uiuc.edu/

Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the Software), to deal with
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Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimers.

Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimers in the documentation
and/or other materials provided with the distribution.

Neither the names of Theoretical and Computational Biophysics Group,
University of Illinois at Urbana-Champaign, nor the names of its contributors
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THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS WITH THE SOFTWARE.

==========================================================================

                 Biopython License Agreement

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
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OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE


==========================================================================

transformations module
  - transformations.py
  - transformations.c

Copyright (c) 2006, Christoph Gohlke
Copyright (c) 2006-2010, The Regents of the University of California
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.
* Neither the name of the copyright holders nor the names of any
  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.

==========================================================================

pyqcprot (src/pyqcprot) is released under the following 'BSD 3-clause' licence:

-----------------------------------------------------------------------------
PyQCPROT

    Author(s) of Original Implementation:     
                  Douglas L. Theobald
                  Department of Biochemistry
                  MS 009
                  Brandeis University
                  415 South St
                  Waltham, MA  02453
                  USA

                  dtheobald@brandeis.edu
                  
                  Pu Liu
                  Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
                  665 Stockton Drive
                  Exton, PA  19341
                  USA

                  pliu24@its.jnj.com

                  For the original code written in C see:
                  http://theobald.brandeis.edu/qcp/ 


    Author of Python Port:
                  Joshua L. Adelman
                  Department of Biological Sciences
                  University of Pittsburgh
                  Pittsburgh, PA 15260
                   
                  jla65@pitt.edu

 
    If you use this QCP rotation calculation method in a publication, please
    reference:

      Douglas L. Theobald (2005)
      "Rapid calculation of RMSD using a quaternion-based characteristic
      polynomial."
      Acta Crystallographica A 61(4):478-480.

      Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)
      "Fast determination of the optimal rotational matrix for macromolecular 
      superpositions."
      J. Comput. Chem. 31, 1561-1563. 


    Copyright (c) 2009-2010, Pu Liu and Douglas L. Theobald 
    Copyright (c) 2011       Joshua L. Adelman
    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.
    * Neither the name of the <ORGANIZATION> 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
    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.


==========================================================================

MDAnalysis logo (see doc/sphinx/source/logos)

The MDAnalysis 'Atom' logo was created by Christian Beckstein and is

Copyright (c) 2011 Christian Beckstein

MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a
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To view a copy of this license, visit
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The logo is contained in the file 'mdanalysis-logo.png'.

Derivatives in the files 'mdanalysis-logo-127x55.png',
'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for
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are distributed under the same license as the 'Atom' logo.

==========================================================================