Software Embedded in UCSF Chimera

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Software Embedded in UCSF Chimera

The list below includes links to where you can obtain the source-code distributions for some of the software packages incorporated into Chimera. All of this software comes bundled with the Chimera release; the links are included here mainly for completeness. In principle, you could upgrade to newer versions of these packages, but it is recommended you wait for a new Chimera release instead, primarily because we incorporate bug fixes and enchancements that may not have been added to the directly distributed versions yet.
This list is current as of 27 June 2008.

Packages:
AL2CO, AmberTools, ANTECHAMBER, Autostereo, comtypes, Expat, FFmpeg, Fontconfig, Free UCS Outline Fonts, Freetype, FTGL, HD5, JPEG, libpng, libTIFF, MDTools, Mesa, MMTK, MSMS, netCDF, NumPy, OpenSSL, PIL, POV-Ray, Pmw, pymmlib, PyOpenGL, PyTables, Python, Qhull, Scientific Python, SwishE, Tcl/Tk, Tix, Togl, TR, UnZip, VRML, zlib
Python 2.4.4
The Python programming language and interpreter.
Copyright 1991-1995 by 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 names of Stichting Mathematisch Centrum or CWI or Corporation for National Research Initiatives or CNRI not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission.
While CWI is the initial source for this software, a modified version is made available by the Corporation for National Research Initiatives (CNRI) at the Internet address ftp://ftp.python.org.
STICHTING MATHEMATISCH CENTRUM AND CNRI DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM OR CNRI 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.

Tcl/Tk 8.4.16
A GUI toolkit.
This software is copyrighted by the Regents of the University of California, Sun Microsystems, Inc., and other parties. The following terms apply to all files associated with the software unless explicitly disclaimed in individual files.
The authors hereby grant permission to use, copy, modify, distribute, and license this software and its documentation for any purpose, provided that existing copyright notices are retained in all copies and that this notice is included verbatim in any distributions. No written agreement, license, or royalty fee is required for any of the authorized uses. Modifications to this software may be copyrighted by their authors and need not follow the licensing terms described here, provided that the new terms are clearly indicated on the first page of each file where they apply.
IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
GOVERNMENT USE: If you are acquiring this software on behalf of the U.S. government, the Government shall have only "Restricted Rights" in the software and related documentation as defined in the Federal Acquisition Regulations (FARs) in Clause 52.227.19 (c) (2). If you are acquiring the software on behalf of the Department of Defense, the software shall be classified as "Commercial Computer Software" and the Government shall have only "Restricted Rights" as defined in Clause 252.227-7013 (c) (1) of DFARs. Notwithstanding the foregoing, the authors grant the U.S. Government and others acting in its behalf permission to use and distribute the software in accordance with the terms specified in this license.

Tix 8.4 CVS
The Tk Interface eXtension.
Copyright (c) 1993-1999 Ioi Kim Lam.
Copyright (c) 2000-2001 Tix Project Group.
Copyright (c) 2004 ActiveState

This software is copyrighted by the above entities and other parties. The following terms apply to all files associated with the software unless explicitly disclaimed in individual files.
The authors hereby grant permission to use, copy, modify, distribute, and license this software and its documentation for any purpose, provided that existing copyright notices are retained in all copies and that this notice is included verbatim in any distributions. No written agreement, license, or royalty fee is required for any of the authorized uses. Modifications to this software may be copyrighted by their authors and need not follow the licensing terms described here, provided that the new terms are clearly indicated on the first page of each file where they apply.
IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
GOVERNMENT USE: If you are acquiring this software on behalf of the U.S. government, the Government shall have only "Restricted Rights" in the software and related documentation as defined in the Federal Acquisition Regulations (FARs) in Clause 52.227.19 (c) (2). If you are acquiring the software on behalf of the Department of Defense, the software shall be classified as "Commercial Computer Software" and the Government shall have only "Restricted Rights" as defined in Clause 252.227-7013 (c) (1) of DFARs. Notwithstanding the foregoing, the authors grant the U.S. Government and others acting in its behalf permission to use and distribute the software in accordance with the terms specified in this license.
Parts of this software are based on the Tcl/Tk software copyrighted by the Regents of the University of California, Sun Microsystems, Inc., and other parties. The original license terms of the Tcl/Tk software distribution is included in the file docs/license.tcltk.
Parts of this software are based on the HTML Library software copyrighted by Sun Microsystems, Inc. The original license terms of the HTML Library software distribution is included in the file docs/license.html_lib.

Togl 2.0 CVS
A OpenGL GUI for Tk.
This software is copyrighted by Brian Paul (brian@mesa3d.org), Benjamin Bederson (bederson@cs.umd.edu), and Greg Couch (gregcouch@users.sourceforge.net). The following terms apply to all files associated with the software unless explicitly disclaimed in individual files.
The authors hereby grant permission to use, copy, modify, distribute, and license this software and its documentation for any purpose, provided that existing copyright notices are retained in all copies and that this notice is included verbatim in any distributions. No written agreement, license, or royalty fee is required for any of the authorized uses. Modifications to this software may be copyrighted by their authors and need not follow the licensing terms described here, provided that the new terms are clearly indicated on the first page of each file where they apply.
IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

PIL 1.1.6
The Python Imaging Library.
Copyright (c) 1997-1999 by Secret Labs AB
Copyright (c) 1995-1999 by Fredrik Lundh
By obtaining, using, and/or copying this software and/or its associated documentation, you agree that you have read, understood, and will comply with the following terms and conditions:
Permission to use, copy, modify, and distribute this software and its associated documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appears in all copies, and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of Secret Labs AB or the author not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission.
SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR 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.

NumPy 1.0.4
The Numeric Python extensions.
Copyright (c) 2005, 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, 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 NumPy Developers 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.

Pmw 1.3
Tk GUI elements written Python.

Copyright 1997-1999 Telstra Corporation Limited, Australia
Copyright 2000-2002 Really Good Software Pty Ltd, Australia

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.

msms 1.3
Fast Molecular Surfaces.
Copyright M.F. Sanner (March 2000).

VRML 2.0 Parser

Portions of this software are based in part on the VRML Parser written by Silicon Graphics, Inc., Mountain View, California, USA.

The Independent JPEG Group's JPEG software

The authors make NO WARRANTY or representation, either express or implied, with respect to this software, its quality, accuracy, merchantability, or fitness for a particular purpose. This software is provided "AS IS", and you, its user, assume the entire risk as to its quality and accuracy.
This software is copyright (C) 1991-1998, Thomas G. Lane. All Rights Reserved except as specified below.
Permission is hereby granted to use, copy, modify, and distribute this software (or portions thereof) for any purpose, without fee, subject to these conditions: (1) If any part of the source code for this software is distributed, then this README file must be included, with this copyright and no-warranty notice unaltered; and any additions, deletions, or changes to the original files must be clearly indicated in accompanying documentation. (2) If only executable code is distributed, then the accompanying documentation must state that "this software is based in part on the work of the Independent JPEG Group". (3) Permission for use of this software is granted only if the user accepts full responsibility for any undesirable consequences; the authors accept NO LIABILITY for damages of any kind.
These conditions apply to any software derived from or based on the IJG code, not just to the unmodified library. If you use our work, you ought to acknowledge us.
Permission is NOT granted for the use of any IJG author's name or company name in advertising or publicity relating to this software or products derived from it. This software may be referred to only as "the Independent JPEG Group's software".
We specifically permit and encourage the use of this software as the basis of commercial products, provided that all warranty or liability claims are assumed by the product vendor.

MDTools 0.65
Molecular dynamics utilities, used by Chimera to read PSF/DCD files (i.e.CHARMM, NAMD, and X-PLOR trajectories).

MDTools for Python is written by James Christopher Phillips of the Theoretical Biophysics Group at the University of Illinois. The group is a National Institutes of Health Resource for Concurrent Biological Computing and is a member of the National Science Foundation Grand Challenge Application Group in Structural Biology. J.C.P. is supported by the United States Department of Energy Computational Science Graduate Fellowship Program. MDTools for Python and related documentation Copyright (c) 1995-96 by University of Illinois Board of Trustees and others. Distribution is encouraged as long as proper credit is given.

MMTK 2.5.23
The Python Molecular Modelling Toolkit, used by Chimera to read MMTK netCDF trajectories.

MMTK is maintained by Konrad Hinsen under the CeCILL FREE SOFTWARE LICENSE AGREEMENT dated 2005-05-21.

UnZip 5.52
UnZip is an extraction utility for archives compressed in .zip format. On Unix-like platforms, the installation program uses a slightly modified UnZip to read zip files. Info-ZIP's software (Zip, UnZip and related utilities) is free and can be be obtained as source code or executables.

(C) 1995-1998 Jean-loup Gailly and Mark Adler
This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
1. 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.
2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
Jean-loup Gailly Mark Adler
jloup@gzip.org madler@alumni.caltech.edu

Mesa 3D Graphics Library 6.5.2
Mesa is an open-source implementation of the OpenGL specification. The main Mesa license is as follows:
Copyright (C) 1999-2007  Brian Paul   All Rights Reserved.

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
BRIAN PAUL 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.
Other parts of Mesa that chimera uses are licensed with the SGI Free Software License B version 1.1.
TR 1.1
TR - OpenGL Tile Rendering Library.
The TR library is copyrighted by Brian Paul under the GNU Library General Public License Version 2, June 1991.

ScientificPython 2.7.8
ScientificPython is a collection of Python modules that are useful for scientific applications.
Scientific Python is licenced under the CeCILL FREE SOFTWARE LICENSE AGREEMENT dated 2005-05-21.

netCDF version 3.6.1 Network Common Data Form.
The Unidata network Common Data Form (netCDF) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface.
Copyright 1993-1999 University Corporation for Atmospheric Research/Unidata
Portions of this software were developed by the Unidata Program at the University Corporation for Atmospheric Research.
Access and use of this software shall impose the following obligations and understandings on the user. The user is granted the right, without any fee or cost, to use, copy, modify, alter, enhance and distribute this software, and any derivative works thereof, and its supporting documentation for any purpose whatsoever, provided that this entire notice appears in all copies of the software, derivative works and supporting documentation. Further, UCAR requests that the user credit UCAR/Unidata in any publications that result from the use of this software or in any product that includes this software. The names UCAR and/or Unidata, however, may not be used in any advertising or publicity to endorse or promote any products or commercial entity unless specific written permission is obtained from UCAR/Unidata. The user also understands that UCAR/Unidata is not obligated to provide the user with any support, consulting, training or assistance of any kind with regard to the use, operation and performance of this software nor to provide the user with any updates, revisions, new versions or "bug fixes."
THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "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 UCAR/UNIDATA 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 ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.

Expat 1.95.8
Expat is an XML parser library written in C.
Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd and Clark Cooper
Copyright (c) 2001, 2002, 2003 Expat maintainers.
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.

Freetype 2.3.5
We use Freetype for antialiased font support.
Portions of this software are copyright © 2007 The FreeType Project (www.freetype.org). All rights reserved.

FTGL 2.1.3svn
A font rendering library for OpenGL.
Copyright © 2001-3 Henry Maddocks
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.

Autostereo
The autostereo package allows applications to use stereo cooperatively on SGI IRIX hardware.
Autostereo is distributed with CGL's Open Source Software License.

OpenSSL 0.9.7l, 0.9.8g
OpenSSL is "a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library."
OpenSSL License
Copyright (c) 1998-2001 The OpenSSL Project. 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.
3. All advertising materials mentioning features or use of this software must display the following acknowledgment: "This product includes software developed by the OpenSSL Project for use in the OpenSSL Toolkit. (http://www.openssl.org/)"
4. The names "OpenSSL Toolkit" and "OpenSSL Project" must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact openssl-core@openssl.org.
5. Products derived from this software may not be called "OpenSSL" nor may "OpenSSL" appear in their names without prior written permission of the OpenSSL Project.
6. Redistributions of any form whatsoever must retain the following acknowledgment: "This product includes software developed by the OpenSSL Project for use in the OpenSSL Toolkit (http://www.openssl.org/)"
THIS SOFTWARE IS PROVIDED BY THE OpenSSL PROJECT ``AS IS'' AND ANY EXPRESSED 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 OpenSSL PROJECT OR ITS 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.
This product includes cryptographic software written by Eric Young (eay@cryptsoft.com). This product includes software written by Tim Hudson (tjh@cryptsoft.com).
Original SSLeay License
Copyright (C) 1995-1998 Eric Young (eay@cryptsoft.com) All rights reserved.
This package is an SSL implementation written by Eric Young (eay@cryptsoft.com). The implementation was written so as to conform with Netscapes SSL.
This library is free for commercial and non-commercial use as long as the following conditions are aheared to. The following conditions apply to all code found in this distribution, be it the RC4, RSA, lhash, DES, etc., code; not just the SSL code. The SSL documentation included with this distribution is covered by the same copyright terms except that the holder is Tim Hudson (tjh@cryptsoft.com).
Copyright remains Eric Young's, and as such any Copyright notices in the code are not to be removed. If this package is used in a product, Eric Young should be given attribution as the author of the parts of the library used. This can be in the form of a textual message at program startup or in documentation (online or textual) provided with the package.
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 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.
3. All advertising materials mentioning features or use of this software must display the following acknowledgement: "This product includes cryptographic software written by Eric Young (eay@cryptsoft.com)" The word 'cryptographic' can be left out if the routines from the library being used are not cryptographic related :-).
4. If you include any Windows specific code (or a derivative thereof) from the apps directory (application code) you must include an acknowledgement: "This product includes software written by Tim Hudson (tjh@cryptsoft.com)"
THIS SOFTWARE IS PROVIDED BY ERIC YOUNG ``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 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.
The licence and distribution terms for any publically available version or derivative of this code cannot be changed. i.e. this code cannot simply be copied and put under another distribution licence [including the GNU Public Licence.]

FFmpeg 0.4.9-pre1
FFmpeg is a complete solution to record, convert and stream audio and video. It includes libavcodec, the leading audio/video codec library. FFmpeg is developed under Linux, but it can compiled under most operating systems, including Windows.

FFmpeg License
FFmpeg is licensed under the GNU Lesser General Public License, or LGPL. Essentially, this means that you are allowed to use the FFmpeg library in your own application, regardless of your application's license. However, if you alter the FFmpeg library in any way, and subsequently distribute it, you are expected to make those changes available under the LGPL license. This is the full text of the LGPL.
Be advised that FFmpeg incorporates several modules that are covered under The GNU General Public License, notably liba52 and libpostproc. If you use these components in your project, you are expected to release your whole application under the GPL if you distribute your project at all. This is the full text of the GPL.

Trademark
FFmpeg is a trademark of Fabrice Bellard, originator of the FFmpeg project.

AL2CO 1.0
AL2CO is a program to compute per-column conservation given a sequence alignment and is in the public domain.

libTIFF 3.8.0
TIFF Library and Utilities.
Copyright (c) 1988-1997 Sam Leffler
Copyright (c) 1991-1997 Silicon Graphics, Inc.
Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that (i) the above copyright notices and this permission notice appear in all copies of the software and related documentation, and (ii) the names of Sam Leffler and Silicon Graphics may not be used in any advertising or publicity relating to the software without the specific, prior written permission of Sam Leffler and Silicon Graphics.
THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Swish-e 2.4.3
Simple Web Indexing System for Humans - Enhanced
While swish-e is licensed with the GNU Public License, we only distribute libsiwsh-e which has the following exception:
As a special exception, the copyright holders of Swish-e give you permission to link Swish-e with independent modules that communicate with Swish-e solely through the libswish-e API interface, regardless of the license terms of these independent modules, and to copy and distribute the resulting combined work under terms of your choice, provided that every copy of the combined work is accompanied by, or provides a URL link to, a complete copy of the source code of Swish-e (the version of Swish-e used to produce the combined work), being distributed under the terms of the GNU General Public License plus this exception. An independent module is a module which is not derived from or based on Swish-e.

SwishE 0.4
The only licensing information is from the PKG-INFO file:
License: BSD

Qhull 2003.1
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram.
Qhull, Copyright (c) 1993-2003
The National Science and Technology Research Center for Computation and Visualization of Geometric Structures (The Geometry Center) University of Minnesota
email: qhull@qhull.org
This software includes Qhull from The Geometry Center. Qhull is copyrighted as noted above. Qhull is free software and may be obtained via http from www.qhull.org. It may be freely copied, modified, and redistributed under the following conditions:
1. All copyright notices must remain intact in all files.
2. A copy of this text file must be distributed along with any copies of Qhull that you redistribute; this includes copies that you have modified, or copies of programs or other software products that include Qhull.
3. If you modify Qhull, you must include a notice giving the name of the person performing the modification, the date of modification, and the reason for such modification.
4. When distributing modified versions of Qhull, or other software products that include Qhull, you must provide notice that the original source code may be obtained as noted above.
5. There is no warranty or other guarantee of fitness for Qhull, it is provided solely "as is". Bug reports or fixes may be sent to qhull_bug@qhull.org; the authors may or may not act on them as they desire.

PyOpenGL 2.0.1.09
PyOpenGL is the cross platform Python binding to OpenGL and related APIs. The only licensing information is from the PKG-INFO file:
License: License :: OSI Approved :: BSD License

AmberTools 1.0
AmberTools is a suite of programs for carrying out complete molecular mechanics investigations.
AmberTools is provided under the GNU General Public License, Version 2.

ANTECHAMBER 1.27
Antechamber is a suite of programs for molecular-mechanics studies.
Antechamber is provided under the GNU General Public License, Version 2.

libpng 1.2.16
libpng is the official PNG reference library.
License: Open Source

POV-Ray 3.6.1
The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics.
POV-Ray is covered by a User License and a Distribution License.

Python Macromolecular Library (mmLib) 0.9.9
mmLib is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
mmLib is made available under the Artistic License without modifications.

Fontconfig 2.5.93
Fontconfig is a library for font customization and configuration.
Copyright © 2001,2003 Keith Packard
Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, 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 Keith Packard not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. Keith Packard makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty.
KEITH PACKARD DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL KEITH PACKARD 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.

Free UCS Outline Fonts, 2008/03/23
Free UCS Outline fonts are a set of three fonts: a sans-serif, a serif, and a fixed width font. They are licensed with the GNU Public License v2 or later and the following exception:
"As a special exception, if you create a document which uses this font, and embed this font or unaltered portions of this font into the document, this font does not by itself cause the resulting document to be covered by the GNU General Public License. This exception does not however invalidate any other reasons why the document might be covered by the GNU General Public License. If you modify this font, you may extend this exception to your version of the font, but you are not obligated to do so. If you do not wish to do so, delete this exception statement from your version."

comtypes 0.4.1
Python COM package, based on the ctypes FFI library.
It is licensed with the MIT license.

HD5 1.6.5
NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities.
Copyright Notice and License terms.

PyTables 2.0
PyTables is a package for managing hierarchical datasets.
Copyright (c) 2002, 2003, 2004 Francesc Altet Copyright (c) 2005, 2006, 2007 Carabos Coop. V. 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 Carabos Coop. V. 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 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.

zlib 1.2.3
zlib compression library.
© 1995-2004 Jean-loup Gailly and Mark Adler
This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:

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.
Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
This notice may not be removed or altered from any source distribution.
Jean-loup Gailly Mark Adler
jloup@gzip.org madler@alumni.caltech.edu