Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Core Wrapper
Upstream-Contact: sw-help@rcsb.rutgers.edu,
 Vladimir Guranovic <vladimir@rcsb.rutgers.edu>
Source: http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html

Files: debian/*
Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
License: GPL-3+

Files: regex/*
Copyright: Copyright 1992, 1993, 1994, 1997 Henry Spencer.  All rights reserved.
License: L1
 This software is not subject to any license of the American Telephone
 and Telegraph Company or of the Regents of the University of California.
 .
 Permission is granted to anyone to use this software for any purpose on
 any computer system, and to alter it and redistribute it, subject
 to the following restrictions:
 .
 1. The author is not responsible for the consequences of use of this
    software, no matter how awful, even if they arise from flaws in it.
 .         
 2. The origin of this software must not be misrepresented, either by
    explicit claim or by omission.  Since few users ever read sources,
    credits must appear in the documentation.
 .
 3. Altered versions must be plainly marked as such, and must not be
    misrepresented as being the original software.  Since few users
    ever read sources, credits must appear in the documentation.
 .         
 4. This notice may not be removed or altered.

Files: cctbx/*
Copyright: Copyright (c) 2006, The Regents of the University of
 California, through Lawrence Berkeley National Laboratory (subject to
 receipt of any required approvals from the U.S. Dept. of Energy).  All
 rights reserved.
License: L2
 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.
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 (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) Neither the name of the University of California, Lawrence Berkeley
 National Laboratory, U.S. Dept. of Energy 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.
 .
 You are under no obligation whatsoever to provide any bug fixes, 
 patches, or upgrades to the features, functionality or performance of
 the source code ("Enhancements") to anyone; however, if you choose to
 make your Enhancements available either publicly, or directly to
 Lawrence Berkeley National Laboratory, without imposing a separate
 written license agreement for such Enhancements, then you hereby grant
 the following license: a  non-exclusive, royalty-free perpetual license
 to install, use, modify, prepare derivative works, incorporate into 
 other computer software, distribute, and sublicense such enhancements or 
 derivative works thereof, in binary and source code form.

Files: test/*
Copyright: John Westbrook
Comment: http://creativecommons.org/licenses/by/3.0/legalcode
License: CC-BY-3.0
 License
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 THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
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 BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
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 1. Definitions
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     "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be considered an Adaptation for the purpose of this License. For the avoidance of doubt, where the Work is a musical work, performance or phonogram, the synchronization of the Work in timed-relation with a moving image ("synching") will be considered an Adaptation for the purpose of this License.
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     "Distribute" means to make available to the public the original and copies of the Work or Adaptation, as appropriate, through sale or other transfer of ownership.
     "Licensor" means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.
     "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being the person or legal entity who first fixes the sounds of a performance or other sounds; and, (iii) in the case of broadcasts, the organization that transmits the broadcast.
     "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without words; a cinematographic work to which are assimilated works expressed by a process analogous to cinematography; a work of drawing, painting, architecture, sculpture, engraving or lithography; a photographic work to which are assimilated works expressed by a process analogous to photography; a work of applied art; an illustration, map, plan, sketch or three-dimensional work relative to geography, topography, architecture or science; a performance; a broadcast; a phonogram; a compilation of data to the extent it is protected as a copyrightable work; or a work performed by a variety or circus performer to the extent it is not otherwise considered a literary or artistic work.
     "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
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     "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium.
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 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws.
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 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:
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     to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections;
     to create and Reproduce Adaptations provided that any such Adaptation, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified.";
     to Distribute and Publicly Perform the Work including as incorporated in Collections; and,
     to Distribute and Publicly Perform Adaptations.
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     For the avoidance of doubt:
         Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;
         Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and,
         Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License.
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 The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved.
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 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
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     You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You must keep intact all notices that refer to this License and to the disclaimer of warranties with every copy of the Work You Distribute or Publicly Perform. When You Distribute or Publicly Perform the Work, You may not impose any effective technological measures on the Work that restrict the ability of a recipient of the Work from You to exercise the rights granted to that recipient under the terms of the License. This Section 4(a) applies to the Work as incorporated in a Collection, but this does not require the Collection apart from the Work itself to be made subject to the terms of this License. If You create a Collection, upon notice from any Licensor You must, to the extent practicable, remove from the Collection any credit as required by Section 4(b), as requested. If You create an Adaptation, upon notice from any Licensor You must, to the extent practicable, remove from the Adaptation any credit as required by Section 4(b), as requested.
     If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribution ("Attribution Parties") in Licensor's copyright notice, terms of service or by other reasonable means, the name of such party or parties; (ii) the title of the Work if supplied; (iii) to the extent reasonably practicable, the URI, if any, that Licensor specifies to be associated with the Work, unless such URI does not refer to the copyright notice or licensing information for the Work; and (iv) , consistent with Section 3(b), in the case of an Adaptation, a credit identifying the use of the Work in the Adaptation (e.g., "French translation of the Work by Original Author," or "Screenplay based on original Work by Original Author"). The credit required by this Section 4 (b) may be implemented in any reasonable manner; provided, however, that in the case of a Adaptation or Collection, at a minimum such credit will appear, if a credit for all contributing authors of the Adaptation or Collection appears, then as part of these credits and in a manner at least as prominent as the credits for the other contributing authors. For the avoidance of doubt, You may only use the credit required by this Section for the purpose of attribution in the manner set out above and, by exercising Your rights under this License, You may not implicitly or explicitly assert or imply any connection with, sponsorship or endorsement by the Original Author, Licensor and/or Attribution Parties, as appropriate, of You or Your use of the Work, without the separate, express prior written permission of the Original Author, Licensor and/or Attribution Parties.
     Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to the Work which would be prejudicial to the Original Author's honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any exercise of the right granted in Section 3(b) of this License (the right to make Adaptations) would be deemed to be a distortion, mutilation, modification or other derogatory action prejudicial to the Original Author's honor and reputation, the Licensor will waive or not assert, as appropriate, this Section, to the fullest extent permitted by the applicable national law, to enable You to reasonably exercise Your right under Section 3(b) of this License (right to make Adaptations) but not otherwise.
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 5. Representations, Warranties and Disclaimer
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 UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO SUCH EXCLUSION MAY NOT APPLY TO YOU.
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 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
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 7. Termination
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     This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
     Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above.
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 8. Miscellaneous
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     Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.
     Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License.
     If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.
     No term or provision of this License shall be deemed waived and no breach consented to unless such waiver or consent shall be in writing and signed by the party to be charged with such waiver or consent.
     This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any communication from You. This License may not be modified without the mutual written agreement of the Licensor and You.
     The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take effect in the relevant jurisdiction in which the License terms are sought to be enforced according to the corresponding provisions of the implementation of those treaty provisions in the applicable national law. If the standard suite of rights granted under applicable copyright law includes additional rights not granted under this License, such additional rights are deemed to be included in the License; this License is not intended to restrict the license of any rights under applicable law.

Files: *
Copyright: RUTGERS
License: RUTGERS_RCSB_PDB_SOFTWARE_LICENSE_AGREEMENT
                RCSB PDB SOFTWARE LICENSE AGREEMENT
 .
 BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING 
 THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE  
 SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS 
 BECOMING A PARTY TO THIS AGREEMENT.  IF LICENSEE DOES NOT 
 AGREE TO ALL OF THE TERMS OF THIS AGREEMENT
 THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE.
 .
 1. LICENSE AGREEMENT
 .
 This is a license between you ("Licensee") and the Protein Data Bank (PDB) 
 at Rutgers, The State University of New Jersey (hereafter referred to 
 as "RUTGERS").   The software is owned by RUTGERS and protected by 
 copyright laws, and some elements are protected by laws governing 
 trademarks, trade dress and trade secrets, and may be protected by 
 patent laws. 
 .
 2. LICENSE GRANT
 .
 RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free 
 perpetual license to install, use, modify, prepare derivative works, 
 incorporate into other computer software, and distribute in binary 
 and source code format, or any derivative work thereof, together with 
 any associated media, printed materials, and on-line or electronic 
 documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), 
 subject to the following terms and conditions: (i) any distribution 
 of the SOFTWARE shall bind the receiver to the terms and conditions 
 of this Agreement; (ii) any distribution of the SOFTWARE in modified 
 form shall clearly state that the SOFTWARE has been modified from 
 the version originally obtained from RUTGERS.  
 .
 2. COPYRIGHT; RETENTION OF RIGHTS.  
 .
 The above license grant is conditioned on the following: (i) you must 
 reproduce all copyright notices and other proprietary notices on any 
 copies of the SOFTWARE and you must not remove such notices; (ii) in 
 the event you compile the SOFTWARE, you will include the copyright 
 notice with the binary in such a manner as to allow it to be easily 
 viewable; (iii) if you incorporate the SOFTWARE into other code, you 
 must provide notice that the code contains the SOFTWARE and include 
 a copy of the copyright notices and other proprietary notices.  All 
 copies of the SOFTWARE shall be subject to the terms of this Agreement.  
 .
 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS 
 .
 RUTGERS is under no obligation whatsoever to: (i) provide maintenance 
 or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches, 
 or upgrades to the features, functionality or performance of the 
 SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS 
 or third parties.  If, in its sole discretion, RUTGERS makes an 
 Enhancement available to you and RUTGERS does not separately enter 
 into a written license agreement with you relating to such bug fix, 
 patch or upgrade, then it shall be deemed incorporated into the SOFTWARE 
 and subject to this Agreement. You are under no obligation whatsoever 
 to provide any Enhancements to RUTGERS or the public that you may 
 develop over time; however, if you choose to provide your Enhancements 
 to RUTGERS, or if you choose to otherwise publish or distribute your 
 Enhancements, in source code form without contemporaneously requiring 
 end users or RUTGERS to enter into a separate written license agreement 
 for such Enhancements, then you hereby grant RUTGERS a non-exclusive,
 royalty-free perpetual license to install, use, modify, prepare
 derivative works, incorporate into the SOFTWARE or other computer
 software, distribute, and sublicense your Enhancements or derivative
 works thereof, in binary and source code form.
 .
 4. FEES.  There is no license fee for the SOFTWARE.  If Licensee
 wishes to receive the SOFTWARE on media, there may be a small charge
 for the media and for shipping and handling.  Licensee is
 responsible for any and all taxes.
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 5. TERMINATION.  Without prejudice to any other rights, Licensor
 may terminate this Agreement if Licensee breaches any of its terms
 and conditions.  Upon termination, Licensee shall destroy all
 copies of the SOFTWARE.
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 6. PROPRIETARY RIGHTS.  Title, ownership rights, and intellectual
 property rights in the Product shall remain with RUTGERS.  Licensee 
 acknowledges such ownership and intellectual property rights and will 
 not take any action to jeopardize, limit or interfere in any manner 
 with RUTGERS' ownership of or rights with respect to the SOFTWARE.  
 The SOFTWARE is protected by copyright and other intellectual 
 property laws and by international treaties.  Title and related 
 rights in the content accessed through the SOFTWARE is the property 
 of the applicable content owner and is protected by applicable law.  
 The license granted under this Agreement gives Licensee no rights to such
 content.
 .
 7. DISCLAIMER OF WARRANTY.  THE SOFTWARE IS PROVIDED FREE OF 
 CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF 
 ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT 
 IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE 
 OR NON-INFRINGING.  THE ENTIRE RISK AS TO THE QUALITY AND 
 PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE.  SHOULD THE 
 SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT 
 LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR.  
 THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF 
 THIS AGREEMENT.  NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER 
 EXCEPT UNDER THIS DISCLAIMER.
 .
 8. LIMITATION OF LIABILITY.  TO THE MAXIMUM EXTENT PERMITTED BY
 APPLICABLE LAW,  IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY 
 INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 
 OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, 
 WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK 
 STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL 
 OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE
 POSSIBILITY THEREOF. 

License: GPL-3+
 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 <http://www.gnu.org/licenses/>.
 .
 On Debian systems, the complete text of the GNU General
 Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.

