Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Jmol Upstream-Contact: http://www.jmol.org Source: https://jmol.sourceforge.net/download/ Disclaimer: The recommended way to cite Jmol is: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ Comment: - This package was debianized on Sun, 28 May 2006 23:30:51 +0200 by Steffen Moeller . - Excluding docbook-xsl and jar files, which are dependencies. We use Debian system libs instead. -About JSmol: Peter Ertl to Ximin Luo : "The underlying Java source is unfortunately due to various legacy legal reasons not available." Can't figure out how to generate in a DFSG way, JSmol disabled for now. - About jcfl-*-source and HPTouchSmart: Can't distribute in Debian (no source code, or license is not free) - JmolColorPocker.js contains very-long-lines. - translations.tgz is a generated file - removing cruft (among other, obscure JS code) in j2s and site-resources Files-Excluded: jars **/*.jar */appletweb */jsmol.zip */src/com/sparshui/cpp/HPTouchSmart/* */jmol.mac */src/org/openscience/jmol/app/webexport/html/JmolColorPicker.js j2s site-resources site-resources-zip Files: * Copyright: 1998-2023 The Jmol Development Team License: LGPL-2.1+ Files: src/javajs/img/GifEncoder.java Copyright: 1996-1998 Jef Poskanzer 2000-2005 The Jmol Development Team License: BSD-2-clause and LGPL-2.1+ Files: src/javajs/img/Jpg64Encoder.java src/javajs/img/JpgEncoder.java src/javajs/util/Base64.java Copyright: 1998 James R. Weeks and BioElectroMech. License: BSD-2-clause Files: src/javajs/img/PpmEncoder.java Copyright: 1996-1998 Jef Poskanzer License: BSD-2-clause Files: src/javajs/util/A4.java src/javajs/util/M3.java src/javajs/util/M4.java src/javajs/util/P3.java src/javajs/util/P3i.java src/javajs/util/P4.java src/javajs/util/T3.java src/javajs/util/T3d.java src/javajs/util/T3i.java src/javajs/util/T4.java src/javajs/util/V3.java src/javajs/util/V3d.java Copyright: 1997-1999 Kenji Hiranabe, Eiwa System Management, Inc. License: custom 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. Kenji Hiranabe and Eiwa System Management,Inc. makes no representations about the suitability of this software for any purpose. It is provided "AS IS" with NO WARRANTY. Files: src/javajs/util/BS.java Copyright: 1995-2007 Sun Microsystems, Inc. License: GPL-2 with Classpath exception Files: src/javajs/util/BinaryDocument.java src/javajs/util/CompoundDocument.java src/javajs/util/Eigen.java src/org/jmol/adapter/* src/org/jmol/bspt/* src/org/jmol/export/Export3D.java src/org/jmol/g3d/* src/org/jmol/i18n/* src/org/jmol/modelsetbio/AlphaMonomer.java src/org/jmol/modelsetbio/CarbohydrateMonomer.java src/org/jmol/render/AxesRenderer.java src/org/jmol/render/BbcageRenderer.java src/org/jmol/render/CageRenderer.java src/org/jmol/render/FontLineShapeRenderer.java src/org/jmol/render/UccageRenderer.java src/org/jmol/renderbio/CartoonRenderer.java src/org/jmol/renderbio/NucleicRenderer.java src/org/jmol/renderbio/RibbonsRenderer.java src/org/jmol/renderbio/StrandsRenderer.java src/org/jmol/rendercgo/* src/org/jmol/renderspecial/DrawRenderer.java src/org/jmol/rendersurface/Plot3DRenderer.java src/org/jmol/rendersurface/PmeshRenderer.java src/org/jmol/script/ScriptEval.java src/org/jmol/script/ScriptMathProcessor.java src/org/jmol/shape/Axes.java src/org/jmol/shape/Bbcage.java src/org/jmol/shape/Uccage.java src/org/jmol/shape/Mesh.java src/org/jmol/shapebio/Strands.java src/org/jmol/shapecgo/* src/org/jmol/shapespecial/DrawMesh.java src/org/jmol/shapesurface/* src/org/jmol/symmetry/* src/org/jmol/util/C.java src/org/jmol/util/Elements.java src/org/jmol/util/Font.java src/org/jmol/util/Geodesic.java src/org/jmol/util/Int2IntHash.java src/org/jmol/util/Normix.java src/org/jmol/util/Point3fi.java src/org/jmol/util/Rgb16.java src/org/jmol/util/SimpleUnitCell.java src/org/jmol/util/Tensor.java src/org/jmol/viewer/ChimeMessenger.java src/org/jmol/viewer/ColorManager.java src/org/jmol/viewer/JC.java src/org/jmol/viewer/ModelManager.java src/org/jmol/viewer/Viewer.java src/org/jmol/viewer/DataManager.java src/org/jmol/viewer/FileManager.java src/org/jmol/viewer/SelectionManager.java src/org/jmol/viewer/ShapeManager.java src/org/jmol/quantum/* Copyright: 2002-2006 Miguel, Jmol Development, www.jmol.org License: LGPL-2.1+ Files: src/jspecview/* src/org/jmol/awt/AwtG2D.java src/org/jmol/awtjs2d/JsG2D.java Copyright: 2002-2016 The University of the West Indies License: LGPL-2.1+ Files: src/jspecview/application/ApplicationMenu.java src/jspecview/application/JSpecView.java src/jspecview/application/MainFrame.java Copyright: 2002-2012 The JSpecView Development Team License: LGPL-2.1+ Files: src/org/jmol/jvxl/* src/org/openscience/* Copyright: 2007 Miguel, Bob, Jmol Development License: LGPL-2.1+ Files: src/jspecview/common/JSVZipUtil.java src/jspecview/common/PDFWriter.java src/jspecview/common/JSVersion.java src/org/jmol/g3d/Pixelator.java src/org/jmol/g3d/PixelatorScreened.java src/org/jmol/g3d/PixelatorShaded.java src/org/jmol/g3d/PixelatorT.java src/org/jmol/i18n/Language.java src/org/jmol/jvxl/readers/XmlReader.java src/org/jmol/quantum/QMAtom.java src/org/jmol/quantum/QS.java src/org/jmol/quantum/SlaterData.java Copyright: 2000-2017 The Jmol Development Team License: LGPL-2.1+ Files: src/jspecview/java/* src/jspecview/js2d/* src/jspecview/popup/* src/org/jmol/shapecgo/CGO.java src/org/jmol/shapesurface/Plot3D.java src/org/jmol/shapesurface/Pmesh.java src/org/jmol/symmetry/CIPChirality.java src/org/jmol/symmetry/SymmetryDesc.java src/org/jmol/symmetry/SymmetryInfo.java src/org/openscience/jmol/* src/org/openscience/jvxl/Jvxl.java src/org/openscience/jvxl/simplewriter/ASimpleJvxlWriter.java Copyright: 2000-2017 The Jmol Development Team License: LGPL-2.1+ Files: src/jspecview/java/AwtDialogFileFilter.java src/jspecview/java/AwtG2D.java src/jspecview/java/AwtPanel.java src/jspecview/java/AwtPrintDialog.java src/jspecview/js2d/JsG2D.java src/jspecview/js2d/JsPanel.java Copyright: 2002-2016 The University of the West Indies License: LGPL-2.1+ Files: src/org/apache/* Copyright: Apache Software Foundation License: Apache-2.0 Files: src/org/jmol/adapter/readers/xml/XmlMolproReader.java Copyright: 2005 Peter Knowles 2003-2005 Miguel, Jmol Development, www.jmol.org License: LGPL-2.1+ Files: src/org/jmol/adapter/readers/xtal/AimsReader.java Copyright: 2011 Joerg Meyer, TU Muenchen 2009 Joerg Meyer, FHI Berlin 2003-2005 Miguel, Jmol Development, www.jmol.org License: LGPL-2.1+ Files: src/org/jmol/adapter/readers/xtal/CrystalReader.java src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java src/org/jmol/adapter/readers/xtal/VaspOutcarReader.java Copyright: 2009 Piero Canepa, University of Kent, UK 2003-2005 Miguel, Jmol Development, www.jmol.org License: LGPL-2.1+ Files: src/org/jmol/atomdata/* Copyright: 2007 Miguel, Bob, Jmol Development License: LGPL-2.1+ Files: src/org/jmol/quantum/NMRNoeMatrix.java src/org/openscience/jmol/app/janocchio/* Copyright: 2007 Eli Lilly and Co. 2002-2006 The Jmol Development Team License: LGPL-2.1+ Files: src/org/openscience/jmol/app/janocchio/NMR_JmolPanel.java Copyright: 2000-2017 The Jmol Development Team License: LGPL-2.1+ Files: src/org/molecularplayground/* Copyright: 2011 University of Massachusetts Comment: We have asked the original authors to clarify the license. https://github.com/molecular-playground/Presenter/issues/1 License: LGPL-2.1+ Files: src/org/openscience/jmol/app/webexport/html/* Copyright: 2000-2017 The Jmol Development Team License: CC-BY-SA-3.0 Files: src/org/jmol/minimize/forcefield/data/UFF.txt Copyright: 2008 The Jmol Development Team 2008 Bob Hanson 2007-2008 Geoffrey R. Hutchison 2007-2008 Tim Vandermeersch Comment: Original source from https://github.com/openbabel/openbabel, unknown which exact commit License: GPL-2 Files: src/org/jmol/minimize/forcefield/data/mmff94.par.txt src/org/jmol/minimize/forcefield/mmff/validate/MMFF94SYMB.PAR src/org/jmol/minimize/forcefield/mmff/validate/*.mol2 Copyright: 1994-1996 Merck and Co., Inc. Comment: Original source from ftp://ftp.wiley.com/public/journals/jcc/suppmat/17/490/MMFF-I_AppendixA.html ftp://ftp.wiley.com/public/journals/jcc/suppmat/17/490/MMFF-I_AppendixB.ascii http://server.ccl.net/cca/data/MMFF94/ License: scientific-data-merck Original authors could not be reached at the advertised email addresses. Tom Halgren , Simon Kearsley The data is freely available at the above web/ftp addresses, assume that distribution is fine. In the worst case, we can replace our copies with scripts that download them at runtime. Files: src/org/jmol/translation/* Copyright: 1998-2012 The Jmol Development Team 2008-2012 Rosetta Contributors (partial) 2008-2012 Canonical Ltd (partial) License: LGPL-2.1+ Files: debian/* Copyright: 2016 Ximin Luo 2010-2016 The debichem team 2006 Steffen Moeller 2004-2005 Daniel Leidert 2021-2024 Pierre Gruet License: GPL-2+ Files: debian/net.sourceforge.jmol.jmol.metainfo.xml Copyright: 2022-2024 Pierre Gruet License: CC-BY-4.0 License: BSD-2-clause 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, all files included with the source code, 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. . 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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. License: CC-BY-4.0 Creative Commons Attribution 4.0 International Public License . By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. . Section 1 -- Definitions. . a. Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image. . b. Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License. . c. Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights. . d. Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements. . e. Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material. . f. Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License. . g. Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license. . h. Licensor means the individual(s) or entity(ies) granting rights under this Public License. . i. Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them. . j. Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world. . k. You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning. . Section 2 -- Scope. . a. License grant. . 1. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to: . a. reproduce and Share the Licensed Material, in whole or in part; and . b. produce, reproduce, and Share Adapted Material. . 2. Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions. . 3. Term. The term of this Public License is specified in Section 6(a). . 4. Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a) (4) never produces Adapted Material. . 5. Downstream recipients. . a. Offer from the Licensor -- Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License. . b. No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material. . 6. No endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i). . b. Other rights. . 1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise. . 2. Patent and trademark rights are not licensed under this Public License. . 3. To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties. . Section 3 -- License Conditions. . Your exercise of the Licensed Rights is expressly made subject to the following conditions. . a. Attribution. . 1. If You Share the Licensed Material (including in modified form), You must: . a. retain the following if it is supplied by the Licensor with the Licensed Material: . i. identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated); . ii. a copyright notice; . iii. a notice that refers to this Public License; . iv. a notice that refers to the disclaimer of warranties; . v. a URI or hyperlink to the Licensed Material to the extent reasonably practicable; . b. indicate if You modified the Licensed Material and retain an indication of any previous modifications; and . c. indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License. . 2. You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information. . 3. If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable. . 4. If You Share Adapted Material You produce, the Adapter's License You apply must not prevent recipients of the Adapted Material from complying with this Public License. . Section 4 -- Sui Generis Database Rights. . Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material: . a. for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database; . b. if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and . c. You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database. . For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights. . Section 5 -- Disclaimer of Warranties and Limitation of Liability. . a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS, IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU. . b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION, NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT, INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES, COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR IN PART, THIS LIMITATION MAY NOT APPLY TO YOU. . c. The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability. . Section 6 -- Term and Termination. . a. This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically. . b. Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates: . 1. automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or . 2. upon express reinstatement by the Licensor. . For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License. . c. For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License. . d. Sections 1, 5, 6, 7, and 8 survive termination of this Public License. . Section 7 -- Other Terms and Conditions. . a. The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed. . b. Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License. . Section 8 -- Interpretation. . a. For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License. . b. To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. . c. No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. . d. Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.