LICENSE

Athena is Copyright (c) 2019-2020, Laboratory of Professor Mark Bathe,
Massachusetts Institute of Technology, and is licensed under the terms
of the GNU GPL version 3, reproduced below.

Athena includes a Python implementation the Earcut library,
copied from https://github.com/joshuaskelly/earcut-python
Earcut is copyright (c) 2016, MapBox [ISC License]

Athena includes code from Orange, https://github.com/biolab/orange3
Orange is copyright (c) 2016 Bioinformatics Laboratory, University of Ljubljana,
                             Faculty of Computer and Information Science [GPL3 License]

Athena includes code adapted from Open-Source PyMOL,
https://github.com/schrodinger/pymol-open-source
Open-Source PyMOL is copyright (c) Schrodinger, LLC. [PyMOL License]

Athena includes code adapted from Qt3D's published example projects.
Qt's example project are copyright (c) 2018 The Qt Company Ltd. [BSD License]

Athena includes a portion of colorTable.py from UCSF Chimera,
by permission of the Chimera developers.  Chimera is copyright
(c) 2000 the Regents of the University of California.

Binary distributions of Athena contain the plyfile Python package,
by Darsh Ranjan, licensed under the GNU GPL version 3.

Binary distributions of Athena contain the NumPy package,
Copyright (C) 2005-2019, NumPy Developers. [NumPy License]

Binary distributions of Athena contain the Qt5 and PySide2 libraries.
The Qt Toolkit is Copyright (C) 2018 The Qt Company Ltd. and other contributors.
Licensed under the GNU Lesser General Public License (LGPL) version 3.

Athena includes an option to generate and save PDB files from the results of
its sequence tools.  In output PDB files, atomic coordinates for nucleic acids
are based on the standard reference frame designed for average A- and B-form
DNA in: WK Olsen, M Bansal, SK Burley, RE Dickerson, M Gerstein, SC Harvey, U
Heinemann, X-J Lu, S Neidle, Z Shakked, H Sklenar, M Suzuki, C-S Tung, E
Westhof, C Wolberger, HM Berman. A standard reference frame for the description
of nucleic acid base-pair geometry. Journal of Molecular Biology 313, 229-237
(2001).


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

ISC License (for earcut code)

Copyright (c) 2016, Mapbox

Permission to use, copy, modify, and/or distribute this software for any purpose
with or without fee is hereby granted, provided that the above copyright notice
and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
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.

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

PyMOL License

 Open-Source PyMOL is Copyright (C) Schrodinger, LLC.

 All Rights Reserved

 Permission to use, copy, modify, distribute, and distribute modified
 versions of this software and its built-in documentation for any
 purpose and without fee is hereby granted, provided that the above
 copyright notice appears in all copies and that both the copyright
 notice and this permission notice appear in supporting documentation,
 and that the name of Schrodinger, LLC not be used in advertising or
 publicity pertaining to distribution of the software without specific,
 written prior permission.

 SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
 INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
 NO EVENT SHALL SCHRODINGER, LLC 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.

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

BSD License (for Qt example code)

Copyright (C) 2018 The Qt Company Ltd.

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
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    the documentation and/or other materials provided with the
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  * Neither the name of The Qt Company Ltd 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
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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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.

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

NumPy License

Copyright (C) 2005-2019, NumPy 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:

  * Redistributions of source code must retain the above copyright notice,
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  * Neither the name of the NumPy Developers nor the names of any contributors
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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
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IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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OF THE POSSIBILITY OF SUCH DAMAGE.

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

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patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.

  Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.

  12. No Surrender of Others' Freedom.

  If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License.  If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all.  For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.

  13. Use with the GNU Affero General Public License.

  Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work.  The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.

  14. Revised Versions of this License.

  The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time.  Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.

  Each version is given a distinguishing version number.  If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation.  If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.

  If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.

  Later license versions may give you additional or different
permissions.  However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.

  15. Disclaimer of Warranty.

  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  16. Limitation of Liability.

  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

  17. Interpretation of Sections 15 and 16.

  If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.

                     END OF TERMS AND CONDITIONS

            How to Apply These Terms to Your New Programs

  If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.

  To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program 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 General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <https://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

  If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

    <program>  Copyright (C) <year>  <name of author>
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.

The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License.  Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".

  You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.

  The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.