License¶
This page contains the End User License Agreement (EULA) of gRINN. Please read and make sure you agree to this agreement before downloading gRINN.
gRINN Developers: Onur Serçinoğlu (onursercin@gmail.com) Pemra Ozbek (pemra.ozbek@marmara.edu.tr)
This End-User License Agreement (“EULA”) is a legal agreement between you and gRINN Developers.
This EULA agreement governs your acquisition and use of our gRINN software (“Software”) directly from gRINN Developers.
Please read this EULA agreement carefully before using the gRINN software. It provides a license to use the gRINN software and contains warranty information and liability disclaimers.
Upon starting the gRINN application, you are confirming your acceptance of the Software and agreeing to become bound by the terms of this EULA agreement.
If you are entering into this EULA agreement on behalf of a company or other legal entity, you represent that you have the authority to bind such entity and its affiliates to these terms and conditions. If you do not have such authority or if you do not agree with the terms and conditions of this EULA agreement, do not use the Software, and you must not accept this EULA agreement.
This EULA agreement shall apply only to the Software supplied by gRINN Developers herewith regardless of whether other software is referred to or described herein. The terms also apply to any gRINN Developers updates, supplements, Internet-based services, and support services for the Software, unless other terms accompany those items on delivery. If so, those terms apply.
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.
License Grant¶
gRINN Developers hereby grants you a personal, non-transferable, non-exclusive licence to use the gRINN software on your devices in accordance with the terms of this EULA agreement.
You are permitted to load the gRINN software under your control. You are responsible for ensuring your device meets the minimum requirements of the gRINN software.
gRINN is free and open to all users.
If you use gRINN for research or commercial purposes, please cite the following publication of gRINN in your publication (article, thesis, etc.):
| [SO2018] | Onur Serçinoğlu, Pemra Ozbek; gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W554–W562, https://doi.org/10.1093/nar/gky381 |
You are not permitted to:¶
- Reproduce, copy, distribute or resell the software.
- Allow any third party to use the Software on behalf of or for the benefit of any third party.
- Use the Software in any way which breaches any applicable local, national or international law.
- use the Software for any purpose that gRINN Developers consider as a breach of this EULA agreement.
Third-party tools included in gRINN:¶
gRINN is based on Python 2.7. Python is available under a Python license:
Python 2.7 license
This is the official license for the Python 2.7 release:
A. HISTORY OF THE SOFTWARE
==========================
Python was created in the early 1990s by Guido van Rossum at Stichting
Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands
as a successor of a language called ABC. Guido remains Python's
principal author, although it includes many contributions from others.
In 1995, Guido continued his work on Python at the Corporation for
National Research Initiatives (CNRI, see http://www.cnri.reston.va.us)
in Reston, Virginia where he released several versions of the
software.
In May 2000, Guido and the Python core development team moved to
BeOpen.com to form the BeOpen PythonLabs team. In October of the same
year, the PythonLabs team moved to Digital Creations (now Zope
Corporation, see http://www.zope.com). In 2001, the Python Software
Foundation (PSF, see http://www.python.org/psf/) was formed, a
non-profit organization created specifically to own Python-related
Intellectual Property. Zope Corporation is a sponsoring member of
the PSF.
All Python releases are Open Source (see http://www.opensource.org for
the Open Source Definition). Historically, most, but not all, Python
releases have also been GPL-compatible; the table below summarizes
the various releases.
Release Derived Year Owner GPL-
from compatible? (1)
0.9.0 thru 1.2 1991-1995 CWI yes
1.3 thru 1.5.2 1.2 1995-1999 CNRI yes
1.6 1.5.2 2000 CNRI no
2.0 1.6 2000 BeOpen.com no
1.6.1 1.6 2001 CNRI yes (2)
2.1 2.0+1.6.1 2001 PSF no
2.0.1 2.0+1.6.1 2001 PSF yes
2.1.1 2.1+2.0.1 2001 PSF yes
2.2 2.1.1 2001 PSF yes
2.1.2 2.1.1 2002 PSF yes
2.1.3 2.1.2 2002 PSF yes
2.2.1 2.2 2002 PSF yes
2.2.2 2.2.1 2002 PSF yes
2.2.3 2.2.2 2003 PSF yes
2.3 2.2.2 2002-2003 PSF yes
2.3.1 2.3 2002-2003 PSF yes
2.3.2 2.3.1 2002-2003 PSF yes
2.3.3 2.3.2 2002-2003 PSF yes
2.3.4 2.3.3 2004 PSF yes
2.3.5 2.3.4 2005 PSF yes
2.4 2.3 2004 PSF yes
2.4.1 2.4 2005 PSF yes
2.4.2 2.4.1 2005 PSF yes
2.4.3 2.4.2 2006 PSF yes
2.5 2.4 2006 PSF yes
2.7 2.6 2010 PSF yes
Footnotes:
(1) GPL-compatible doesn't mean that we're distributing Python under
the GPL. All Python licenses, unlike the GPL, let you distribute
a modified version without making your changes open source. The
GPL-compatible licenses make it possible to combine Python with
other software that is released under the GPL; the others don't.
(2) According to Richard Stallman, 1.6.1 is not GPL-compatible,
because its license has a choice of law clause. According to
CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1
is "not incompatible" with the GPL.
Thanks to the many outside volunteers who have worked under Guido's
direction to make these releases possible.
B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON
===============================================================
PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
--------------------------------------------
1. This LICENSE AGREEMENT is between the Python Software Foundation
("PSF"), and the Individual or Organization ("Licensee") accessing and
otherwise using this software ("Python") in source or binary form and
its associated documentation.
2. Subject to the terms and conditions of this License Agreement, PSF
hereby grants Licensee a nonexclusive, royalty-free, world-wide
license to reproduce, analyze, test, perform and/or display publicly,
prepare derivative works, distribute, and otherwise use Python
alone or in any derivative version, provided, however, that PSF's
License Agreement and PSF's notice of copyright, i.e., "Copyright (c)
2001, 2002, 2003, 2004, 2005, 2006 Python Software Foundation; All Rights
Reserved" are retained in Python alone or in any derivative version
prepared by Licensee.
3. In the event Licensee prepares a derivative work that is based on
or incorporates Python or any part thereof, and wants to make
the derivative work available to others as provided herein, then
Licensee hereby agrees to include in any such work a brief summary of
the changes made to Python.
4. PSF is making Python available to Licensee on an "AS IS"
basis. PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
INFRINGE ANY THIRD PARTY RIGHTS.
5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
6. This License Agreement will automatically terminate upon a material
breach of its terms and conditions.
7. Nothing in this License Agreement shall be deemed to create any
relationship of agency, partnership, or joint venture between PSF and
Licensee. This License Agreement does not grant permission to use PSF
trademarks or trade name in a trademark sense to endorse or promote
products or services of Licensee, or any third party.
8. By copying, installing or otherwise using Python, Licensee
agrees to be bound by the terms and conditions of this License
Agreement.
BEOPEN.COM LICENSE AGREEMENT FOR PYTHON 2.0
-------------------------------------------
BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1
1. This LICENSE AGREEMENT is between BeOpen.com ("BeOpen"), having an
office at 160 Saratoga Avenue, Santa Clara, CA 95051, and the
Individual or Organization ("Licensee") accessing and otherwise using
this software in source or binary form and its associated
documentation ("the Software").
2. Subject to the terms and conditions of this BeOpen Python License
Agreement, BeOpen hereby grants Licensee a non-exclusive,
royalty-free, world-wide license to reproduce, analyze, test, perform
and/or display publicly, prepare derivative works, distribute, and
otherwise use the Software alone or in any derivative version,
provided, however, that the BeOpen Python License is retained in the
Software, alone or in any derivative version prepared by Licensee.
3. BeOpen is making the Software available to Licensee on an "AS IS"
basis. BEOPEN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, BEOPEN MAKES NO AND
DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT
INFRINGE ANY THIRD PARTY RIGHTS.
4. BEOPEN SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF THE
SOFTWARE FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS
AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE, OR ANY
DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
5. This License Agreement will automatically terminate upon a material
breach of its terms and conditions.
6. This License Agreement shall be governed by and interpreted in all
respects by the law of the State of California, excluding conflict of
law provisions. Nothing in this License Agreement shall be deemed to
create any relationship of agency, partnership, or joint venture
between BeOpen and Licensee. This License Agreement does not grant
permission to use BeOpen trademarks or trade names in a trademark
sense to endorse or promote products or services of Licensee, or any
third party. As an exception, the "BeOpen Python" logos available at
http://www.pythonlabs.com/logos.html may be used according to the
permissions granted on that web page.
7. By copying, installing or otherwise using the software, Licensee
agrees to be bound by the terms and conditions of this License
Agreement.
CNRI LICENSE AGREEMENT FOR PYTHON 1.6.1
---------------------------------------
1. This LICENSE AGREEMENT is between the Corporation for National
Research Initiatives, having an office at 1895 Preston White Drive,
Reston, VA 20191 ("CNRI"), and the Individual or Organization
("Licensee") accessing and otherwise using Python 1.6.1 software in
source or binary form and its associated documentation.
2. Subject to the terms and conditions of this License Agreement, CNRI
hereby grants Licensee a nonexclusive, royalty-free, world-wide
license to reproduce, analyze, test, perform and/or display publicly,
prepare derivative works, distribute, and otherwise use Python 1.6.1
alone or in any derivative version, provided, however, that CNRI's
License Agreement and CNRI's notice of copyright, i.e., "Copyright (c)
1995-2001 Corporation for National Research Initiatives; All Rights
Reserved" are retained in Python 1.6.1 alone or in any derivative
version prepared by Licensee. Alternately, in lieu of CNRI's License
Agreement, Licensee may substitute the following text (omitting the
quotes): "Python 1.6.1 is made available subject to the terms and
conditions in CNRI's License Agreement. This Agreement together with
Python 1.6.1 may be located on the Internet using the following
unique, persistent identifier (known as a handle): 1895.22/1013. This
Agreement may also be obtained from a proxy server on the Internet
using the following URL: http://hdl.handle.net/1895.22/1013".
3. In the event Licensee prepares a derivative work that is based on
or incorporates Python 1.6.1 or any part thereof, and wants to make
the derivative work available to others as provided herein, then
Licensee hereby agrees to include in any such work a brief summary of
the changes made to Python 1.6.1.
4. CNRI is making Python 1.6.1 available to Licensee on an "AS IS"
basis. CNRI MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, CNRI MAKES NO AND
DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 1.6.1 WILL NOT
INFRINGE ANY THIRD PARTY RIGHTS.
5. CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1,
OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
6. This License Agreement will automatically terminate upon a material
breach of its terms and conditions.
7. This License Agreement shall be governed by the federal
intellectual property law of the United States, including without
limitation the federal copyright law, and, to the extent such
U.S. federal law does not apply, by the law of the Commonwealth of
Virginia, excluding Virginia's conflict of law provisions.
Notwithstanding the foregoing, with regard to derivative works based
on Python 1.6.1 that incorporate non-separable material that was
previously distributed under the GNU General Public License (GPL), the
law of the Commonwealth of Virginia shall govern this License
Agreement only as to issues arising under or with respect to
Paragraphs 4, 5, and 7 of this License Agreement. Nothing in this
License Agreement shall be deemed to create any relationship of
agency, partnership, or joint venture between CNRI and Licensee. This
License Agreement does not grant permission to use CNRI trademarks or
trade name in a trademark sense to endorse or promote products or
services of Licensee, or any third party.
8. By clicking on the "ACCEPT" button where indicated, or by copying,
installing or otherwise using Python 1.6.1, Licensee agrees to be
bound by the terms and conditions of this License Agreement.
ACCEPT
CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2
--------------------------------------------------
Copyright (c) 1991 - 1995, Stichting Mathematisch Centrum Amsterdam,
The Netherlands. All rights reserved.
Permission to use, copy, modify, and distribute this software and its
documentation for any purpose and without fee is hereby granted,
provided that the above copyright notice appear in all copies and that
both that copyright notice and this permission notice appear in
supporting documentation, and that the name of Stichting Mathematisch
Centrum or CWI not be used in advertising or publicity pertaining to
distribution of the software without specific, written prior
permission.
STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO
THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM 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.
gRINN makes use of and includes several open-source software:
PyQt5 is distributed with gRINN. PyQt5 is dual licensed on all platforms under the Riverbank Commercial License and the GPL v3.
NumPy is distributed with gRINN. NumPy is available under NumPy license:
pandas is distributed with gRINN. pandas is available under BSD 3-Clause License.
networkx is distributed with gRINN. networkx is available under a BSD license:
ProDy is distributed with gRINN. ProDy is available under 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.
MDTraj is distributed with gRINN. MDtraj is available under the LPGL.
PyMol (open source version 1.9.0) is distributed with gRINN. PyMol is available under the CNRI Python License.
matplotlib (v2.0.2) is distributed with gRINN. matplotlib is available under matplotlib license:
1. This LICENSE AGREEMENT is between the Matplotlib Development Team (“MDT”), and the Individual or Organization (“Licensee”) accessing and otherwise using matplotlib software in source or binary form and its associated documentation.
2. Subject to the terms and conditions of this License Agreement, MDT hereby grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use matplotlib 2.0.2 alone or in any derivative version, provided, however, that MDT’s License Agreement and MDT’s notice of copyright, i.e., “Copyright (c) 2012-2013 Matplotlib Development Team; All Rights Reserved” are retained in matplotlib 2.0.2 alone or in any derivative version prepared by Licensee.
3. In the event Licensee prepares a derivative work that is based on or incorporates matplotlib 2.0.2 or any part thereof, and wants to make the derivative work available to others as provided herein, then Licensee hereby agrees to include in any such work a brief summary of the changes made to matplotlib 2.0.2.
4. MDT is making matplotlib 2.0.2 available to Licensee on an “AS IS” basis. MDT MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, MDT MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF MATPLOTLIB 2.0.2 WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
5. MDT SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF MATPLOTLIB 2.0.2 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING MATPLOTLIB 2.0.2, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
6. This License Agreement will automatically terminate upon a material breach of its terms and conditions.
7. Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between MDT and Licensee. This License Agreement does not grant permission to use MDT trademarks or trade name in a trademark sense to endorse or promote products or services of Licensee, or any third party.
8. By copying, installing or otherwise using matplotlib 2.0.2, Licensee agrees to be bound by the terms and conditions of this License Agreement.
Intellectual Property and Ownership¶
gRINN Developers shall at all times retain ownership of the Software as originally downloaded by you and all subsequent downloads of the Software by you. The Software (and the copyright, and other intellectual property rights of whatever nature in the Software, including any modifications made thereto) are and shall remain the property of gRINN Developers.
gRINN Developers reserves the right to grant licences to use the Software to third parties.
Termination¶
This EULA agreement is effective from the date you first use the Software and shall continue until terminated. You may terminate it at any time upon written notice to gRINN Developers.
It will also terminate immediately if you fail to comply with any term of this EULA agreement. Upon such termination, the licenses granted by this EULA agreement will immediately terminate and you agree to stop all access and use of the Software. The provisions that by their nature continue and survive will survive any termination of this EULA agreement.
Governing Law¶
This EULA agreement, and any dispute arising out of or in connection with this EULA agreement, shall be governed by and construed in accordance with the laws of Republic of Turkey.