Main Licence: // CCP4 Molecular Graphics Program // This library is free software: you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public License // version 3, modified in accordance with the provisions of the // license to address the requirements of UK law. // You should have received a copy of the modified GNU Lesser General // Public License along with this library. If not, copies may be // downloaded from http://www.ccp4.ac.uk/ccp4license.php // 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 Lesser General Public License for more details. This program also contains CCP4 libraries distributed under the same licence. ============================================================================ This program is linked against the libungif, libjpeg, libpng and libz dll's, which may also be in the distribution. The following licenses apply. This software is based in part on the work of the Independent JPEG Group. This software distribution includes the zlib library, (C) 1995-2002 Jean-loup Gailly and Mark Adler. libpng Copyright (c) 2000-2002 Glenn Randers-Pehrson. ============================================================================ This program may also be linked against the libbzip2, The dll bzip2.dll may be in the distribution. -------------------------------------------------------------------------- This program, "bzip2", the associated library "libbzip2", and all documentation, are copyright (C) 1996-2007 Julian R Seward. 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. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 3. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 4. 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. Julian Seward, jseward@bzip.org bzip2/libbzip2 version 1.0.5 of 10 December 2007 -------------------------------------------------------------------------- ============================================================================ This program also contains Python (www.python.org). This may be Python version 2.2, 2.3, 2.4, 2.5. The licences for the particular versions follow: 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 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. ================================================================================ This software uses the GPL v3. version of Qt, Copyright (C) 2008 Nokia Corporation and/or its subsidiary(-ies) and PyQt4, Copyright (C) Riverbank Software, but with the following clause: Additional rights granted beyond the GPL (the "Exception"). As a special exception to the terms and conditions of GPL version 2.0 or GPL version 3.0, Nokia Corporation hereby grants you the rights described below, provided you agree to the terms and conditions in this Exception, including its obligations and restrictions on use. Nothing in this Exception gives you or anyone else the right to change the licensing terms of the Qt Open Source Edition. Below, "Licensed Software" shall refer to the software licensed under the GPL version 2.0 or GPL version 3.0 and this exception. 1) The right to use open source licenses not compatible with the GNU General Public License version 2.0 or GNU General Public License version 3.0: You may link software (hereafter referred to as "Your Software") against the Licensed Software and/or distribute binaries of Your Software linked against the Licensed Software, provided that: A) Your Software is licensed under one of the following licenses: License name Version(s)/Copyright Date Academic Free License 2.0, 2.1, 3.0 Apache Software License 1.0 or 1.1 Apache License 2.0 Apple Public Source License 2.0 Artistic license (as set forth in the addendum file) BSD license "July 22 1999" Common Development and Distribution License (CDDL) 1.0 Common Public License 1.0 Eclipse Public License 1.0 GNU Library or "Lesser" General Public License (LGPL) 2.0, 2.1, 3.0 Jabber Open Source License 1.0 MIT License (as set forth in the addendum file) Mozilla Public License (MPL) 1.0 or 1.1 Open Software License 2.0, 3.0 OpenSSL license (with original SSLeay license) "2003" ("1998") PHP License 3.0 Python license (CNRI Python License) (as set forth in the addendum file) Python Software Foundation License 2.1.1 Q Public License 1.0 Sleepycat License "1999" W3C License "2001" X11 License X11R6.6 Zlib/libpng License (as set forth in the addendum file) Zope Public License 2.0, 2.1 (Licenses without a specific version number or date are reproduced in the file GPL_Exception_Addendum.txt in your source package). and B) You must, on request, make a complete package including the complete source code of Your Software (as defined in the GNU General Public License version 2, section 3, but excluding anything excluded by the special exception in the same section) available to Nokia Corporation under the same license as that granted to other recipients of the source code of Your Software. and C) Your or any other contributor's rights to: i) distribute the source code of Your Software to anyone for any purpose; and ii) publicly discuss the development project for Your Software and its goals in any form and in any forum are not prohibited by any legal instrument, including but not limited to contracts, non-disclosure agreements, and employee contracts. 2) The right to link non-open source applications with pre-installed versions of the Licensed Software: You may link applications with binary pre-installed versions of the Licensed Software, provided that such applications have been developed and are deployed in accordance with the terms and conditions of the Qt Commercial License Agreement. ================================================================================ This program also contains a complete distribution of ImageMagick, to which the following licence applies: Copyright 1999-2010 ImageMagick Studio LLC Licensed under the ImageMagick License (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.imagemagick.org/script/license.php Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ================================================================================ Uses the NCBI BLAST service provided by the European Bioinformatics Institute (EBI). Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp302 Nucl. Acids Res. (2010) 38 (suppl 2): W695-W699. doi: 10.1093/nar/gkq313 However, the connection to this service provided by CCP4MG is not supported by EBI: All problems with running blast should be reported to CCP4MG support. ================================================================================ This program may also come with the Biopython software to which the following license applies. 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. ================================================================================