debian/0000755000000000000000000000000012050173047007165 5ustar debian/jmol-applet.dirs0000644000000000000000000000011512047717505012302 0ustar usr/bin usr/lib/cgi-bin usr/share/jmol-applet usr/share/doc/jmol-applet/html debian/libjmol-java-doc.dirs0000644000000000000000000000004312047717505013170 0ustar usr/share/doc/libjmol-java-doc/api debian/jmol.docs0000644000000000000000000000003111615225515010776 0ustar COPYRIGHT.txt README.txt debian/examples/0000755000000000000000000000000012047717505011014 5ustar debian/examples/demo.html0000644000000000000000000000041712047717505012630 0ustar jmol applet atoms demo

caffeine

debian/examples/caffeine.xyz0000644000000000000000000000216612047717505013335 0ustar 24 Caffeine H -3.3804130 -1.1272367 0.5733036 N 0.9668296 -1.0737425 -0.8198227 C 0.0567293 0.8527195 0.3923156 N -1.3751742 -1.0212243 -0.0570552 C -1.2615018 0.2590713 0.5234135 C -0.3068337 -1.6836331 -0.7169344 C 1.1394235 0.1874122 -0.2700900 N 0.5602627 2.0839095 0.8251589 O -0.4926797 -2.8180554 -1.2094732 C -2.6328073 -1.7303959 -0.0060953 O -2.2301338 0.7988624 1.0899730 H 2.5496990 2.9734977 0.6229590 C 2.0527432 -1.7360887 -1.4931279 H -2.4807715 -2.7269528 0.4882631 H -3.0089039 -1.9025254 -1.0498023 H 2.9176101 -1.8481516 -0.7857866 H 2.3787863 -1.1211917 -2.3743655 H 1.7189877 -2.7489920 -1.8439205 C -0.1518450 3.0970046 1.5348347 C 1.8934096 2.1181245 0.4193193 N 2.2861252 0.9968439 -0.2440298 H -0.1687028 4.0436553 0.9301094 H 0.3535322 3.2979060 2.5177747 H -1.2074498 2.7537592 1.7203047 debian/jmol.install0000644000000000000000000000026712047717505011534 0ustar build/jmol usr/bin debian/jmol.desktop usr/share/applications build/doc/JmolUserGuide/*.html usr/share/doc/jmol/html/en/ build/doc/JmolUserGuide_fr/*.html usr/share/doc/jmol/html/fr/ debian/jmol-applet.README.Debian0000644000000000000000000000242112047717505013461 0ustar jmol-applet for Debian ---------------------- To setup a server running the Jmol applet, easily do the following: 1) Create an Alias which points to /usr/share/jmol-applet e.g. for Apache: Alias /jmol /usr/share/jmol-applet and if necessary, adjust the path to JmolAppletProxy.cgi (which is originally located /usr/lib/cgi-bin) in JmolApplet.properties. OR copy the content of /usr/share/jmol-applet to a directory of your choice. The JmolAppletProxy.cgi script is located in /usr/share/cgi-bin. Depending on your provided: copy it into a script-directory and adjust the path in JmolApplet.properties. 2) Now use Jmol.js as you want in your websites. Documentation for the JavaScript library is provided at: http://jmol.sourceforge.net/jslibrary/. The package contains a short example under examples. Easily copy these files in a (server-)directory of your choice (e.g. test/), adjust the path to the applet directory (it now points to ../jmol) and start your browser with the related URL (e.g. your-domain.tld/test/demo.html). Further documentation is provided at http://www.jmol.org. -- Daniel Leidert (dale) , Thu, 4 Feb 2005 23:31:02 +0100 debian/rules0000755000000000000000000000172512047717505010263 0ustar #!/usr/bin/make -f # -*- makefile -*- #export DH_VERBOSE=1 export JAVA_HOME:= /usr/lib/jvm/default-java %: dh $@ --with=javahelper --buildsystem=ant --parallel override_dh_auto_build: (cd jars && for i in /usr/share/java/*.jar /usr/share/icedtea-web/*.jar; \ do ln -s $$i; done) dh_auto_build -- -Dvecmath.jar=vecmath.jar -Ditext.jar=itext1.jar \ -Dcommons-cli.jar=commons-cli.jar jar applet-jar doc override_dh_auto_install: dh_auto_install install -D -m664 src/org/openscience/jmol/app/images/icon.png \ $(CURDIR)/debian/jmol/usr/share/pixmaps/jmol-icon.png install -D -m775 appletweb/chime2jmol_old.pl \ $(CURDIR)/debian/jmol-applet/usr/bin/chime2jmol install -D -m775 appletweb/JmolAppletProxy.cgi \ $(CURDIR)/debian/jmol-applet/usr/lib/cgi-bin/JmolAppletProxy.cgi override_dh_clean: $(RM) -r build dh_clean jars/* src/org/jmol/translation/translations.tgz find . -name "*.jar" -delete debian/libjmol-java-doc.install0000644000000000000000000000006312047717505013677 0ustar build/javadoc/* usr/share/doc/libjmol-java-doc/api debian/control0000644000000000000000000000713012047717500010575 0ustar Source: jmol Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck , Daniel Leidert Build-Depends: ant, ant-contrib, debhelper (>> 8), default-jdk, docbook-xml (>> 4.2), docbook-xsl (>> 1.66), icedtea-plugin, javahelper, libcommons-cli-java, libitext1-java, libjaxp1.3-java, libnaga-java, libsaxon-java, libvecmath-java, xsltproc Standards-Version: 3.9.3 Homepage: http://jmol.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/jmol/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/jmol/ DM-Upload-Allowed: yes Package: jmol Architecture: all Depends: libjmol-java, ${misc:Depends} Description: Molecular Viewer Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry. . File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP. Package: libjmol-java Section: java Architecture: all Depends: ${java:Depends}, ${misc:Depends} Suggests: libjmol-java-doc Description: Java library for molecular structures Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry. . This package contains the Jmol Java libraries. Package: jmol-applet Section: java Architecture: all Depends: default-jre | java2-runtime, libjmol-java, libwww-perl, ${misc:Depends}, ${perl:Depends} Description: Jmol Java applet Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry. . File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP. . This package contains the Jmol Java applet Package: libjmol-java-doc Section: doc Architecture: all Depends: ${misc:Depends} Description: API documentation for libjmol-java Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry. . This package comprises the javadoc documentation for the libjmol-java package. debian/changelog0000644000000000000000000000675512050173034011050 0ustar jmol (12.2.32+dfsg2-1) unstable; urgency=low * New repackaged upstream tarball, removing the src/com/json directory due to licensing issues (closes: #692622). * debian/patches/remove_json.patch: New patch, adapting the codebase to the removal of the src/com/json package, taken from upstream revision 17710. * debian/get-orig-source.sh: Remove src/com/json directory when repackaging. -- Michael Banck Mon, 12 Nov 2012 14:14:02 +0100 jmol (12.2.32+dfsg-1) unstable; urgency=low * New upstream release. -- Daniel Leidert Fri, 29 Jun 2012 20:41:26 +0200 jmol (12.2.30+dfsg-1) unstable; urgency=low * New upstream release. * debian/chime2jmol.1.xml: Turned into debian/chime2jmol.1. * debian/jmol.1.xml: Turned into debian/jmol.1. * debian/compat: Bumped level to 8. * debian/control (Standards-Version): Bumped to 3.9.3. (Build-Depends): Increased dh version. (Depends): Fixed needless-dependency-on-jre. Added libwww-perl for CGI script. (Section): Fixed binary-control-field-duplicates-source. (Uploaders): Added myself. * debian/copyright: Massive update. * debian/jmol.doc-base: Adjusted. * debian/jmol.install: Path fix. * debian/jmol-applet.doc-base: Added. * debian/jmol-applet.install: Install applet guide. * debian/menu: Renamed to debian/jmol.menu. * debian/rules: Rewritten for dh 8 including addons. Set JAVA_HOME (closes: #678057). * debian/upstream: Added. * debian/patches/*.patch: Added header tags. * debian/README.source: Added. * debian/get-orig-source.sh: Also remove .exe, .dll and non-free sources. -- Daniel Leidert Sun, 24 Jun 2012 22:39:20 +0200 jmol (12.2.18+dfsg-1) unstable; urgency=low * New upstream point release. -- Michael Banck Mon, 19 Mar 2012 23:08:08 +0100 jmol (12.2.2+dfsg-1) unstable; urgency=low * New upstream release; Closes: #646253. [ Daniel Leidert ] * debian/control (Standards-Version): Bumped to 3.9.2. (XS-Vcs-*): Renamed to Vcs-*. (Homepage): Dropped duplicated field. * debian/get-orig-source.sh: Remove pre-compiled and source-less stuff. * debian/watch: Only check for stable releases. Handle DFSG compatible versions. [ Michael Banck ] * debian/patches/chime2jmol_binary.patch: Refreshed. * debian/control (jmol): Remove Suggests on jmol-doc, package does not exist. * debian/get-orig-source.sh: Remove newly introduced tools/*.jar as well. * debian/control (Build-Depends): Added icedtea-plugin; Closes: #628292. * debian/source/include-binaries: Update. * debian/control (Build-Depends): Added libnaga-java. * debian/rules (build-stamp): Symlink all required jars into jars/ prior to build and do no longer define ${lib.dir}. * debian/rules (clean): Remove jar symlinks from jars/. * debian/rules (install): Account for rename of chime2jmol.pl to chime2jmol_old.pl. -- Michael Banck Mon, 31 Oct 2011 20:53:01 +0100 jmol (12.1.42-1) experimental; urgency=low * New upstream development release; Closes: #623075. -- Michael Banck Sun, 17 Apr 2011 12:20:33 +0200 jmol (12.0.40-1) unstable; urgency=low * New upstream release. * debian/patches/missing_directories.patch: Dropped, no longer needed. -- Michael Banck Mon, 11 Apr 2011 22:04:43 +0200 jmol (12.0.28-1) unstable; urgency=low * Initial release; Closes: #512930. -- Michael Banck Sun, 30 Jan 2011 16:13:29 +0100 debian/libjmol-java.jlibs0000644000000000000000000000004211615225515012561 0ustar build/Jmol.jar build/JmolData.jar debian/jmol.menu0000644000000000000000000000021512047717505011023 0ustar ?package(jmol):needs="X11" section="Applications/Science/Chemistry"\ title="jmol" command="/usr/bin/jmol" \ longtitle="Molecular Viewer" debian/jmol-applet.doc-base0000644000000000000000000000051312047717505013020 0ustar Document: jmol-applet Title: Jmol Applet Documentation Author: The Jmol Development Team Abstract: This manual describes the functionality and usage of the Jmol applet. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/jmol-applet/html/JmolAppletGuide.html Files: /usr/share/doc/jmol-applet/html/JmolAppletGuide.html debian/watch0000644000000000000000000000050011615225515010215 0ustar # accept both old tarballs with jmol-... and newer with Jmol-... # only check for non-pre-releases, which means the middle number is even # don't check for RCs version=3 opts=dversionmangle=s/\+dfsg$// \ http://sf.net/jmol/[jJ]mol-([\d]+\.[\d]*[02468]+\.[\d]+)-full\.tar\.gz \ debian /bin/sh debian/get-orig-source.sh debian/get-orig-source.sh0000644000000000000000000000154512050172576012547 0ustar #!/bin/sh set -ex UPSTREAM_VERSION=$2 ORIG_TARBALL=$3 REAL_TARBALL=`readlink -f ${ORIG_TARBALL}` WORKING_DIR=`dirname ${ORIG_TARBALL}` ORIG_TARBALL_DFSG=`echo ${ORIG_TARBALL} | sed -e "s/\(${UPSTREAM_VERSION}\)\(\.orig\)/\1+dfsg\2/g"` ORIG_TARBALL_DIR=`echo ${ORIG_TARBALL_DFSG} | sed -e "s/_\(${UPSTREAM_VERSION}\)/-\1/g" -e "s/\.tar\.gz//g"` ORIG_TARBALL_DIR_STRIP=`basename ${ORIG_TARBALL_DIR}` mkdir -p ${ORIG_TARBALL_DIR} tar --directory=${ORIG_TARBALL_DIR} --strip 1 -xzf ${REAL_TARBALL} || exit 1 rm -f ${ORIG_TARBALL} ${REAL_TARBALL} ant -f ${ORIG_TARBALL_DIR}/build.xml clean find ${ORIG_TARBALL_DIR}/ -name "*.jar" -o -name "*.exe" -o -name "*.dll" -o -name "jcfl-*.tar.gz" | xargs rm -f rm -rf ${ORIG_TARBALL_DIR}/src/com/json GZIP=-9 tar --remove-files --directory ${WORKING_DIR} -czf ${ORIG_TARBALL_DFSG} ${ORIG_TARBALL_DIR_STRIP} || exit 1 exit 0 debian/jmol-applet.install0000644000000000000000000000031112047717505013005 0ustar build/JmolApplet*.jar usr/share/jmol-applet build/doc/JmolAppletGuide*.html usr/share/doc/jmol-applet/html appletweb/Jmol.js usr/share/jmol-applet appletweb/JmolApplet.properties usr/share/jmol-applet debian/libjmol-java-doc.doc-base0000644000000000000000000000057012047717505013711 0ustar Document: libjmol-java-doc Title: Jmol Library Documentation Author: The Jmol Development Team Abstract: This manual contains the API documentation for libjmol-java, the library for the molecule and crystal 3D-viewer and animator jmol. Section: Programming Format: HTML Index: /usr/share/doc/libjmol-java-doc/api/index.html Files: /usr/share/doc/libjmol-java-doc/api/*.html debian/upstream0000644000000000000000000000077412047717505010771 0ustar Name: Jmol Homepage: http://www.jmol.org Bug-Database: http://sourceforge.net/tracker/?group_id=23629&atid=379133 Cite-As: "Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/" Contact: jmol-developers@lists.sourceforge.net FAQ: http://jmol.sourceforge.net/faqs/ Gallery: http://jmol.sourceforge.net/screenshots/ Repository: https://jmol.svn.sourceforge.net/svnroot/jmol/ Repository-Browse: http://jmol.svn.sourceforge.net/ Screenshots: http://jmol.sourceforge.net/demo/ debian/compat0000644000000000000000000000000212047717505010374 0ustar 8 debian/jmol.manpages0000644000000000000000000000001611615225515011644 0ustar debian/jmol.1 debian/libjmol-java.doc-base0000644000000000000000000000051312047717505013143 0ustar Document: libjmol-java Title: Jmol Developer Guide Author: The Jmol Development Team Abstract: This manual describes the part of the molecule and crystal 3D-viewer and animator jmol. Section: Programming Format: HTML Index: /usr/share/doc/libjmol-java/html/JmolDevelopersGuide.html Files: /usr/share/doc/libjmol-java/html/*.html debian/copyright0000644000000000000000000002710412047717505011135 0ustar Format: http://dep.debian.net/deps/dep5 Upstream-Name: Jmol Upstream-Contact: http://www.jmol.org Source: http://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 . Copyright: 2000-2012, The Jmol Development Team License: LGPL-2.1+ Files: src/* src/com/sparshui/* src/org/jmol/* src/org/openscience/* appletweb/* Copyright: 2000-2012, The Jmol Development Team 1998, Guillaume Cottenceau (partial) 2005, Shravan Sadasivan & Richard Spinney (partial) 2009, Piero Canepa, University of Kent, UK (partial) 2009, 2011, Joerg Meyer, FHI Berlin / TU Muenchen (partial) 2011, University of Massachusetts (partial) Comments: Partial copyright as written above goes for src/org/openscience/molecularplayground/MPJmolApp.java, src/org/jmol/adapter/readers/xtal/AimsReader.java, src/org/jmol/adapter/readers/xtal/CrystalReader.java, src/org/jmol/adapter/readers/xtal/VaspOutcarReader.java, src/org/jmol/adapter/readers/xtal/CastepReader.java, src/org/jmol/jcamp/utils/StringDataUtils.java, src/org/jmol/jcamp/Visua.java License: LGPL-2.1+ Files: src/org/jmol/export/image/GifEncoder.java src/org/jmol/export/image/PpmEncoder.java src/org/jmol/export/image/ImageEncoder.java Copyright: 1996, 1998, Jef Poskanzer License: BSD-2 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. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR 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 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. Files: src/com/json/* Copyright: 2002, 2006, 2008, JSON.org License: MIT/X 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 shall be used for Good, not Evil. . 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. Files: src/com/sparshui/cpp/HPTouchSmart/NWMultiTouch.h Copyright: 2008, NextWindow Ltd. License: BSD-3 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 NextWindow 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 NEXTWINDOW LTD ``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 NEXTWINDOW LTD 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. Files: src/com/obrador/* src/org/jmol/util/Base64.java src/org/jmol/util/JpegEncoder.java Copyright: 1998, James R. Weeks and BioElectroMech License: The JpegEncoder and its associated classes are Copyright (c) 1998, James R. Weeks and BioElectroMech. This software is based in part on the work of the Independent JPEG Group. . 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. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR 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 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. Files: doc/source/xml2po* Copyright: Copyright (C) 2004 Danilo Segan License: GPL-2+ Files: doc/docbook-xml-*.zip Copyright: various Comment: Copyright and License see /usr/share/doc/docbook-xml/copyright. License: other Permission to use, copy, modify and distribute the DocBook XML DTD and its accompanying documentation for any purpose and without fee is hereby granted in perpetuity, provided that the above copyright notice and this paragraph appear in all copies. The copyright holders make no representation about the suitability of the DTD for any purpose. It is provided "as is" without expressed or implied warranty. . If you modify the DocBook DTD in any way, except for declaring and referencing additional sets of general entities and declaring additional notations, label your DTD as a variant of DocBook. See the maintenance documentation for more information. . Please direct all questions, bug reports, or suggestions for changes to the docbook@lists.oasis-open.org mailing list. For more information, see http://www.oasis-open.org/docbook/. Files: doc/docbook-xsl-*.tar.gz Copyright: various Comment: Copyright and License see /usr/share/doc/docbook-xsl/copyright. License: MIT/X 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. . Except as contained in this notice, the names of individuals credited with contribution to this software shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization from the individuals in question. . Any stylesheet derived from this Software that is publicly distributed will be identified with a different name and the version strings in any derived Software will be changed so that no possibility of confusion between the derived package and this Software will exist. . 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 NORMAN WALSH OR ANY OTHER CONTRIBUTOR 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 Files: debian/* Copyright: 2004, 2005, Daniel Leidert 2006 Steffen Moeller 2010-2012 The debichem team License: GPL-2+ License: LGPL-2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems the complete text of the GNU Lesser General Public License 2.1 can be found in the file `/usr/share/common-licenses/LGPL-2.1'. License: GPL-2+ 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 2 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, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On Debian systems the complete text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/libjmol-java.install0000644000000000000000000000007111615225515013126 0ustar build/doc/JmolDev*.html usr/share/doc/libjmol-java/html debian/jmol.dirs0000644000000000000000000000002311615225515011010 0ustar /usr/share/pixmaps debian/jmol.doc-base0000644000000000000000000000046512047717505011543 0ustar Document: jmol Title: Jmol User Guide Author: The Jmol Development Team Abstract: This manual describes the functionality of the molecule and crystal 3D-viewer and animator jmol. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/jmol/html/en/index.html Files: /usr/share/doc/jmol/html/en/*.html debian/jmol-applet.docs0000644000000000000000000000001312047717505012266 0ustar README.txt debian/chime2jmol.10000644000000000000000000000166512047717505011321 0ustar .TH "CHIME2JMOL" "1" "February 04, 2005" .SH "NAME" chime2jmol \- convert chime into jmol scripts .SH "SYNOPSIS" .B chime2jmol [ .BI "\-s " sourcedir " |" .BI "\-d " destdir " |" .B "\-c |" .BI "\-a " archive " |" .BI "\-b " path " |" .B "\-v" ] .TP .B chime2jmol .B usage .SH "DESCRIPTION" .PP .B chime2jmol is a Perl program for converting Chime into JMol scripts. .SH "OPTIONS" .PP The following options are currently supported: .TP .B usage Show summary of options. .TP .BI "\-s " sourcedir Specify source directory. .TP .BI "\-d " destdir Specify destination directory. .TP .B \-c Clear destination directory. .TP .BI "\-a " archive Specify alternate archive name. .TP .BI "\-b " path Specify codebase. .TP .B \-v Be verbose. .SH "AUTHOR" This manual page was written by Daniel Leidert <\&daniel\&.leidert@wgdd\&.de\&> for the Debian GNU/Linux distribution (but may be used by others). debian/source/0000755000000000000000000000000011633231320010460 5ustar debian/source/include-binaries0000644000000000000000000000020511633231320013615 0ustar debian/selfSignedCertificate/selfSignedCertificate.cer debian/selfSignedCertificate/selfSignedCertificate.store debian/jmol-icon.png debian/source/format0000644000000000000000000000001411615225515011677 0ustar 3.0 (quilt) debian/libjmol-java.dirs0000644000000000000000000000005711615225515012425 0ustar usr/share/java usr/share/doc/libjmol-java/html debian/jmol-applet.examples0000644000000000000000000000006712047717505013165 0ustar debian/examples/demo.html debian/examples/caffeine.xyz debian/README.source0000644000000000000000000000042112047717505011352 0ustar jmol source for Debian ---------------------- The source package needs to be re-packed to remove shipped binary stuff: .jar, .exe and .dll files. Also the jcf source tarball is removed, because its license is non-free. -- Daniel Leidert , June 2012 debian/jmol-applet.links0000644000000000000000000000010312047717505012456 0ustar usr/share/jmol-applet/JmolApplet.jar usr/share/java/JmolApplet.jar debian/jmol-applet.manpages0000644000000000000000000000002412047717505013133 0ustar debian/chime2jmol.1 debian/patches/0000755000000000000000000000000012050171236010612 5ustar debian/patches/ant-contrib_classpath.patch0000644000000000000000000000143312047717500016124 0ustar Author: debichem-devel@lists.alioth.debian.org Description: Fix the path to systems ant-contrib.jar --- a/tools/build-i18n.xml +++ b/tools/build-i18n.xml @@ -9,7 +9,7 @@ - + --- a/build.xml +++ b/build.xml @@ -7,7 +7,7 @@ - + debian/patches/cgi_fix_shebang.patch0000644000000000000000000000663712047717500014754 0ustar Author: debichem-devel@lists.alioth.debian.org Description: Fix shebang line by using dos2unix --- a/appletweb/JmolAppletProxy.cgi +++ b/appletweb/JmolAppletProxy.cgi @@ -1,49 +1,49 @@ -#!/usr/bin/perl -# -# $RCSfile$ -# $Author: michaelthoward $ -# $Date: 2003-08-19 20:44:26 +0200 (mar., 19 août 2003) $ -# $Revision: 1299 $ -# -# Copyright (C) 2003 The Jmol Development Team -# -# Contact: jmol-developers@lists.sf.net -# -# This library is free software; you can redistribute it and/or -# modify it under the terms of the GNU Lesser General Public -# License as published by the Free Software Foundation; either -# version 2.1 of the License, or (at your option) any later version. -# -# This library is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this library; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA -# 02111-1307 USA. -# -use English; -use CGI; -use CGI::Carp; -use LWP; -use LWP::UserAgent; -use strict; - -my $cgi = new CGI; -my $url = $cgi->param('url'); -if (! $url) { - print $cgi->header(-type=>'text/plain' -status=>'404 Not Found'); -} -my $userAgent = LWP::UserAgent->new; -$userAgent->agent("JmolAppletProxy/1.0"); - -my $request = HTTP::Request->new(GET => $url); -my $response = $userAgent->request($request); -if ($response->is_success()) { - print $cgi->header(-type=>'text/plain'), $response->content(); -} else { - print $cgi->header(-type=>'text/plain' -status=>$response->status_line); - print $response->status_line; -} +#!/usr/bin/perl +# +# $RCSfile$ +# $Author: michaelthoward $ +# $Date: 2003-08-19 20:44:26 +0200 (mar., 19 août 2003) $ +# $Revision: 1299 $ +# +# Copyright (C) 2003 The Jmol Development Team +# +# Contact: jmol-developers@lists.sf.net +# +# This library is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public +# License as published by the Free Software Foundation; either +# version 2.1 of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this library; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA +# 02111-1307 USA. +# +use English; +use CGI; +use CGI::Carp; +use LWP; +use LWP::UserAgent; +use strict; + +my $cgi = new CGI; +my $url = $cgi->param('url'); +if (! $url) { + print $cgi->header(-type=>'text/plain' -status=>'404 Not Found'); +} +my $userAgent = LWP::UserAgent->new; +$userAgent->agent("JmolAppletProxy/1.0"); + +my $request = HTTP::Request->new(GET => $url); +my $response = $userAgent->request($request); +if ($response->is_success()) { + print $cgi->header(-type=>'text/plain'), $response->content(); +} else { + print $cgi->header(-type=>'text/plain' -status=>$response->status_line); + print $response->status_line; +} debian/patches/right_cgi_diretory.patch0000644000000000000000000000037512047717500015526 0ustar Author: Daniel Leidert Description: Fix CGI directory --- a/appletweb/JmolApplet.properties +++ b/appletweb/JmolApplet.properties @@ -1 +1 @@ -JmolAppletProxy=JmolAppletProxy.cgi +JmolAppletProxy=/cgi-bin/JmolAppletProxy.cgi debian/patches/series0000644000000000000000000000023112047732414012032 0ustar jmol_search_in_usr_share_java.patch ant-contrib_classpath.patch chime2jmol_binary.patch right_cgi_diretory.patch cgi_fix_shebang.patch remove_json.patch debian/patches/remove_json.patch0000644000000000000000000002062312050171236014164 0ustar --- ./src/org/jmol/viewer/Viewer.java.orig 2012-06-24 23:55:18.000000000 +0200 +++ ./src/org/jmol/viewer/Viewer.java 2012-11-11 14:13:37.815786803 +0100 @@ -7979,7 +7979,7 @@ // synchronized here trapped the eventQueue public Object evaluateExpression(Object stringOrTokens) { - return ScriptEvaluator.evaluateExpression(this, stringOrTokens); + return ScriptEvaluator.evaluateExpression(this, stringOrTokens, false); } public Object getHelixData(BitSet bs, int tokType) { @@ -10039,4 +10039,8 @@ return global.minPixelSelRadius; } + public ScriptVariable evaluateExpressionAsVariable(Object stringOrTokens) { + return (ScriptVariable) ScriptEvaluator.evaluateExpression(this, stringOrTokens, true); + } + } --- ./src/org/jmol/viewer/PropertyManager.java.orig 2012-06-24 23:55:19.000000000 +0200 +++ ./src/org/jmol/viewer/PropertyManager.java 2012-11-11 14:14:26.523786754 +0100 @@ -385,7 +385,7 @@ case PROP_ERROR_MESSAGE: return viewer.getErrorMessageUntranslated(); case PROP_EVALUATE: - return ScriptEvaluator.evaluateExpression(viewer, myParam.toString()); + return ScriptEvaluator.evaluateExpression(viewer, myParam.toString(), false); case PROP_EXTRACT_MODEL: return viewer.getModelExtract(myParam, true, "MOL"); case PROP_FILE_INFO: --- ./src/org/jmol/script/ScriptEvaluator.java.orig 2012-06-24 23:55:19.000000000 +0200 +++ ./src/org/jmol/script/ScriptEvaluator.java 2012-11-11 14:21:55.607786562 +0100 @@ -502,11 +502,12 @@ * * @param viewer * @param expr + * @param asVariable TODO * @return an object of one of the following types: Boolean, Integer, Float, * String, Point3f, BitSet */ - public static Object evaluateExpression(Viewer viewer, Object expr) { + public static Object evaluateExpression(Viewer viewer, Object expr, boolean asVariable) { // Text.formatText for MESSAGE and ECHO ScriptEvaluator e = new ScriptEvaluator(viewer); try { @@ -514,16 +515,17 @@ if (e.compileScript(null, EXPRESSION_KEY + " = " + expr, false)) { e.contextVariables = viewer.getContextVariables(); e.setStatement(0); - return e.parameterExpressionString(2, 0); + return (asVariable ? e.parameterExpressionList(2, -1, false).get(0) : e.parameterExpressionString(2, 0)); } } else if (expr instanceof Token[]) { e.contextVariables = viewer.getContextVariables(); - return e.atomExpression((Token[]) expr, 0, 0, true, false, true, false); + BitSet bs = e.atomExpression((Token[]) expr, 0, 0, true, false, true, false); + return (asVariable ? ScriptVariable.getVariable(bs): bs); } } catch (Exception ex) { Logger.error("Error evaluating: " + expr + "\n" + ex); } - return "ERROR"; + return (asVariable ? ScriptVariable.getVariable("ERROR") : "ERROR"); } ShapeManager shapeManager; --- ./src/org/openscience/jmol/app/jmolpanel/JsonNioService.java.orig 2012-06-24 23:55:18.000000000 +0200 +++ ./src/org/openscience/jmol/app/jmolpanel/JsonNioService.java 2012-11-11 15:21:22.283875205 +0100 @@ -24,21 +24,31 @@ package org.openscience.jmol.app.jmolpanel; +import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.IOException; +import java.io.InputStreamReader; +import java.io.UnsupportedEncodingException; import java.net.InetSocketAddress; import java.util.Calendar; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; import javax.vecmath.Point3f; import org.jmol.api.JmolViewer; +import org.jmol.script.ScriptVariable; +import org.jmol.util.Escape; import org.jmol.util.Logger; import org.jmol.util.TextFormat; +import org.jmol.viewer.Viewer; -import com.json.JSONException; -import com.json.JSONObject; -import com.json.JSONTokener; +//import com.json.JSONException; +//import com.json.JSONObject; +//import com.json.JSONTokener; import naga.ConnectionAcceptor; import naga.NIOServerSocket; @@ -139,7 +149,7 @@ private NIOSocket inSocket; protected NIOSocket outSocket; private NIOServerSocket serverSocket; - private JmolViewer jmolViewer; + JmolViewer jmolViewer; private JsonNioClient client; private boolean wasSpinOn; @@ -320,14 +330,10 @@ } protected void initialize(String role, NIOSocket nioSocket) { - try { JSONObject json = new JSONObject(); json.put("magic", "JmolApp"); json.put("role", role); sendMessage(json, null, nioSocket); - } catch (JSONException e) { - close(); - } } private void startServerService() { @@ -426,15 +432,41 @@ String path = TextFormat.simpleReplace(contentPath, "%ID%", id) .replace('\\', '/'); File f = new File(path); - FileInputStream jsonFile = new FileInputStream(f); Logger.info("JsonNiosService Setting path to " + f.getAbsolutePath()); int pt = path.lastIndexOf('/'); if (pt >= 0) path = path.substring(0, pt); else path = "."; - JSONObject contentJSON = new JSONObject(new JSONTokener(jsonFile)); - String script = contentJSON.getString("startup_script"); + JSONObject contentJSON = null; + try { + BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(f), "UTF-8")); + StringBuilder sb = new StringBuilder(8192); + String line; + while ((line = br.readLine()) != null) + sb.append(line).append('\n'); + br.close(); + contentJSON = new JSONObject(sb.toString()); + } catch (UnsupportedEncodingException e) { + // should not be possible + } + + String script = null; + if (contentJSON.has("scripts")) { + //TODO -- this is not implemented, because JSONObject.getJSONArray is not implemented + List scripts = contentJSON.getJSONArray("scripts"); + for (int i = scripts.size(); --i >= 0;) { + JSONObject scriptInfo = scripts.get(i); + if (scriptInfo.getString("startup").equals("yes")) { + script = scriptInfo.getString("filename"); + break; + } + } + if (script == null) + throw new Exception("scripts startup:yes not found"); + } else { + script = contentJSON.getString("startup_script"); + } Logger.info("JsonNiosService startup_script=" + script); setBanner("", false); jmolViewer.script("exit"); @@ -545,4 +577,56 @@ } } + class JSONObject extends Hashtable{ + + public JSONObject() { + } + + @SuppressWarnings("unchecked") + JSONObject(String msg) throws Exception { + ScriptVariable o = ((Viewer) jmolViewer).evaluateExpressionAsVariable(msg); + if (!(o.value instanceof Map)) + throw new Exception("invalid JSON: " + msg); + putAll((Map) o.value); + } + + boolean has(String key) { + return containsKey(key); + } + + String getString(String key) throws Exception { + return containsKey(key) ? get(key).toString() : null; + } + + @SuppressWarnings("unchecked") + public List getJSONArray(String key) throws Exception { + if (!has(key)) + throw new Exception("JSON key not found:" + key); + List list = new ArrayList(); + List svlist = ((ScriptVariable) get(key)).getList(); + for (int i = 0; i < svlist.size(); i++) + list.add(new JSONObject(Escape.escape((Map)(svlist.get(i).value)))); + return list; + } + + public long getLong(String key) throws Exception { + if (!has(key)) + throw new Exception("JSON key not found:" + key); + return Long.parseLong(get(key).toString()); + } + + public int getInt(String key) throws Exception { + if (!has(key)) + throw new Exception("JSON key not found:" + key); + return Integer.parseInt(get(key).toString()); + } + + public double getDouble(String key) throws Exception { + if (!has(key)) + throw new Exception("JSON key not found:" + key); + return Double.parseDouble(get(key).toString()); + } + + + } } debian/patches/chime2jmol_binary.patch0000644000000000000000000000035412047717500015240 0ustar Author: Daniel Leidert Description: Add a shebang line --- a/appletweb/chime2jmol_old.pl +++ b/appletweb/chime2jmol_old.pl @@ -1,3 +1,4 @@ +#!/usr/bin/perl use strict; use HTML::Parser; use Getopt::Std; debian/patches/jmol_search_in_usr_share_java.patch0000644000000000000000000000060512047717500017672 0ustar Author: debichem-devel@lists.alioth.debian.org Description: If /usr/share/java/Jmol.jar exists use it as jarpath. --- a/jmol +++ b/jmol @@ -15,6 +15,8 @@ jarpath=$JMOL_HOME/Jmol.jar elif [ -f /usr/share/jmol/Jmol.jar ] ; then jarpath=/usr/share/jmol/Jmol.jar +elif [ -f /usr/share/java/Jmol.jar ] ; then + jarpath=/usr/share/java/Jmol.jar else echo Jmol.jar not found exit debian/jmol.10000644000000000000000000000361012047717505010221 0ustar .TH "JMOL" "1" "August 21, 2004" .SH "NAME" jmol \- 3D molecule and crystal viewer .SH "SYNOPSIS" .B jmol .RB [ options ] .RI [ file ] .SH "DESCRIPTION" .PP .B jmol is a program that is able to view 3D chemical information like molecular structures, vibrations of bonds or animations. .SH "OPTIONS" .PP Currently accepted options are: .TP .B \-h, \-\-help Print help on the command line options. .TP .BI "\-g " "WIDTH" "x" "HEIGHT" ", \-\-geometry " "WIDTH" "x" "HEIGHT" Use window-geometry \fIWIDTH\fR x \fIHEIGHT\fR. .TP .BI "\-s " "scriptfile" ", \-\-script " "scriptfile" Run script \fIscriptfile\fR. .TP .BI "\-D" "property" "=" "value" Use \fIvalue\fR for the given \fIproperty\fR (for a list see below). .TP .BI "\-Dcdk.debugging=" "booelan" Set debugging (default: \fIfalse\fR). .TP .BI "\-Dcdk.debug.stdout=" "boolean" Set debug to stdout (default: \fIfalse\fR). .TP .BI "\-Duser.language=" "LANG" Set user language (default: \fIEN\fR). .TP .BI "\-Ddisplay.speed=" "fps|ms" Set display speed in milli seconds (ms) or frames per second (fps) (default: \fIms\fR). .TP .BI "\-DJmolConsole=" "boolean" Start with Jmol-console (default: \fItrue\fR). .TP .BI "\-Dplugin.dir=" "path" Set path to plugin directory (default: unset). By calling the shell wrapper \fI\%/usr/bin/jmol\fR, the directory is set to \fI\%/usr/share/jmol\fR. Plugins installed to \fI\%~/.jmol/plugins\fR are automatically detected. .SH "FILES" .PP .TP .I ~/.jmol/plugins Per-user plugin directory. .SH "SEE ALSO" .PP More information about JMol can be found at \fI\%http://jmol.sourceforge.net/\fR and in \fI\%/usr/share/doc/jmol/html\fR (User-Guide). .SH "AUTHORS" .PP This manual page was written by Egon Willighagen <\&egonw@users\&.sourceforge\&.net\&> and Daniel Leidert <\&daniel\&.leidert@wgdd\&.de\&> for the Debian GNU/Linux distribution (but may be used by others). debian/jmol.desktop0000644000000000000000000000060011615225515011521 0ustar [Desktop Entry] Version=1.0 Name=Jmol Comment=Molecular Viewer Exec=jmol %f Icon=jmol-icon Terminal=false Type=Application Categories=Java;Science;Chemistry;Physics;Education; StartupNotify=true MimeType=chemical/x-cif;chemical/x-cml;chemical/x-gamess-output;chemical/x-gaussian-log;chemical/x-mopac-out;chemical/x-pdb;chemical/x-xyz;chemical/x-gaussian-cube;chemical/x-qchem-output;