debian/0000755000000000000000000000000012211712200007152 5ustar debian/xmakemol-gl.menu0000644000000000000000000000017610674022577012307 0ustar ?package(xmakemol-gl):needs="X11"\ section="Applications/Science/Chemistry"\ title="xmakemol" command="/usr/bin/xmakemol" debian/copyright0000644000000000000000000000422111765152261011126 0ustar This package was debianized by Michael Banck on Sun, 21 Oct 2001 09:29:26 +0000. It was downloaded from: http://www.nongnu.org/xmakemol/ Upstream Author: Matt Hodges Copyright: Copyright (C) 1997-2007 Matthew P. Hodges basename.c: Copyright (C) 1996-1998 Free Software Foundation, Inc. License: GPL v2+ (*/*) 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. On Debian GNU/Linux systems, the complete text of the GNU General Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. License: LGPL 2.1+ (basename.c) 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 On Debian GNU/Linux systems, the complete text of the GNU Lesser General Public License v2.1 can be found in `/usr/share/common-licenses/LGPL-2.1'. debian/xmakemol-gl.doc-base0000644000000000000000000000073311257012430013000 0ustar Document: xmakemol Title: XMakemol Documentation Author: Matthew P. Hodges Abstract: XMakemol is an application for the visualization and manipulation of atomic, molecular, and other chemical systems. The manual covers invocation, menu entries and miscellaneous features. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/xmakemol-gl/xmakemol.html Files: /usr/share/doc/xmakemol-gl/xmakemol.html Format: text Files: /usr/share/doc/xmakemol-gl/xmakemol.txt.gz debian/xmakemol.doc-base0000644000000000000000000000072211257012430012376 0ustar Document: xmakemol Title: XMakemol Documentation Author: Matthew P. Hodges Abstract: XMakemol is an application for the visualization and manipulation of atomic, molecular, and other chemical systems. The manual covers invocation, menu entries and miscellaneous features. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/xmakemol/xmakemol.html Files: /usr/share/doc/xmakemol/xmakemol.html Format: text Files: /usr/share/doc/xmakemol/xmakemol.txt.gz debian/source/0000755000000000000000000000000012211711722010462 5ustar debian/source/format0000644000000000000000000000001411752042436011700 0ustar 3.0 (quilt) debian/xmakemol.desktop0000644000000000000000000000031311257010672012374 0ustar [Desktop Entry] Version=1.0 Name=XMakemol GenericName=Molecule Viewer Comment=View and manipulate atomic and other chemical systems Type=Application Exec=xmakemol Categories=Chemistry;Education;Science; debian/xmakemol.menu0000644000000000000000000000017311146070204011665 0ustar ?package(xmakemol):needs="X11"\ section="Applications/Science/Chemistry"\ title="xmakemol" command="/usr/bin/xmakemol" debian/rules0000755000000000000000000000350512211711663010251 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 COMMON_OPTIONS = --srcdir=.. --program-transform-name='s/\.pl//' COMMON_OPTIONS_normal = --with-mesa --without-opengl COMMON_OPTIONS_opengl = --without-mesa export CPPFLAGS ?= $(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS ?= $(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS ?= $(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS ?= $(shell dpkg-buildflags --get LDFLAGS) -Wl,-z,defs -Wl,--as-needed %: dh $@ --with autotools_dev --parallel override_dh_auto_configure: normal/config.status opengl/config.status %/config.status: configure dh_testdir mkdir $(@D) dh_auto_configure --builddirectory=$(@D) -- $(COMMON_OPTIONS) \ $(if $(findstring $(@D),opengl),$(COMMON_OPTIONS_opengl),$(COMMON_OPTIONS_normal)) \ LDFLAGS="$(LDFLAGS)" override_dh_auto_build: dh_auto_build --builddirectory=normal dh_auto_build --builddirectory=opengl override_dh_auto_install: dh_auto_install --builddirectory=normal -- DESTDIR=$(CURDIR)/debian/xmakemol dh_auto_install --builddirectory=opengl -- DESTDIR=$(CURDIR)/debian/xmakemol-gl # When upstream adds the xmake_anim.pl.1 manpage to the man_MANS variable # we can remove the following steps - the --program-transform-name # configure option will do everything for us. install xmake_anim.pl.1 $(CURDIR)/debian/xmakemol/usr/share/man/man1/xmake_anim.1 install xmake_anim.pl.1 $(CURDIR)/debian/xmakemol-gl/usr/share/man/man1/xmake_anim.1 override_dh_auto_clean: dh_auto_clean $(RM) -r normal/ opengl/ override_dh_clean: dh_clean config.h override_dh_installchangelogs: dh_installchangelogs -A NEWS override_dh_installdocs: dh_installdocs -A PROBLEMS README xmakemol.html xmakemol.txt override_dh_install: dh_install -A debian/xmakemol.desktop usr/share/applications/ override_dh_installexamples: dh_installexamples -A examples/* debian/xmakemol-gl.README.Debian0000644000000000000000000000066311146070204013443 0ustar xmakemol-gl for Debian ---------------------- If you want to change the /usr/share/xmakemol/elements file you should rather copy the file somewhere else and either run xmakemol from that directory or set XM_ELEMENTS to the directory or file. -- Michael Banck , 2001-10-29 xmake_anim.pl is installed as /usr/bin/xmake_anim (Debian Policy Manual, section 10.4). -- LI Daobing , 2007-09-19 debian/watch0000644000000000000000000000017711146070204010217 0ustar # See uscan(1) for format version=3 http://download.savannah.gnu.org/releases-noredirect/xmakemol/xmakemol-([\d\.]+)\.tar\.gz debian/patches/0000755000000000000000000000000012211711722010611 5ustar debian/patches/h-bond-factor.patch0000644000000000000000000000056511752042436014273 0ustar Author: Michael Banck Description: Decrease hydrogen bond factor so intramolecular h-bonds are less likely to be displayed. --- a/globals.h +++ b/globals.h @@ -172,7 +172,7 @@ double bdfd_factor=1.0; double hbdfd_factor=1.0; double ibdfd_factor=1.0; -double ihbdfd_factor=1.0; +double ihbdfd_factor=0.7; double largest_cov_rad; Boolean redraw; debian/patches/series0000644000000000000000000000002411752042436012032 0ustar h-bond-factor.patch debian/changelog0000644000000000000000000002476112211711715011050 0ustar xmakemol (5.16-7) unstable; urgency=low [ Daniel Leidert ] * debian/control (Uploaders): Removed myself. (Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical. (Build-Depends): Added autotools-dev. Replaced libgl1-mesa-swx11-dev by libgl1-mesa-dev, lesstif2-dev by libmotif-dev (closes: #714740, #714447). (Standards-Version): Bumped to 3.9.4. (DM-Upload-Allowed): Dropped. * debian/rules: Use autotools_dev addon, fix outdated-autotools-helper-file. Enable hardening. -- Debichem Team Wed, 04 Sep 2013 22:10:41 +0200 xmakemol (5.16-6) unstable; urgency=low * debian/compat: Increased compatibility level to 7. * debian/control (Standards-Version): Bumped to 3.9.3. (Build-Depends): Increased dh version. Dropped dpatch. (Vcs-Browser): Fixed. (Description): Fixed description-synopsis-starts-with-article. * debian/copyright: Minor update. * debian/rules: Rewritten for dh 7. * debian/patches/03_h-bond-factor.dpatch: Renamed to debian/patches/h-bond-factor.patch. * debian/patches/00list: Renamed to debian/patches/series and adjusted. * debian/source/format: Changed to 3.0 quilt (closes: #664319). -- Daniel Leidert (dale) Sun, 10 Jun 2012 19:13:19 +0200 xmakemol (5.16-5) unstable; urgency=low * debian/control (Build-Depends): Added dpatch. * debian/rules: Include /usr/share/dpatch/dpatch.make and let the build-stamp target depend on patch-stamp. * debian/patches/03_h-bond-factor.dpatch: New patch, decrease hydrogen bond factor so intramolecular h-bonds are less likely to be displayed. -- Michael Banck Wed, 14 Jul 2010 18:10:00 +0200 xmakemol (5.16-4) unstable; urgency=low * debian/control: Bumped to 3.8.3. (Vcs-Svn): Fixed. (Depends): Fixed debhelper-but-no-misc-depends. * debian/rules (%/config.status): Fix configure options for OpenGL-enabled build - a bug introduced by myself in 5.16-2 (closes: #548124). (binary-arch): Removed deprecated dh_desktop. * debian/xmakemol.desktop: Removed Icon field because of non-existent icon (closes: #547966). * debian/xmakemol.doc-base, debian/xmakemol-gl.doc-base: Added. -- Daniel Leidert (dale) Fri, 25 Sep 2009 03:03:32 +0200 xmakemol (5.16-3) unstable; urgency=low * Upload to unstable. * debian/control (Description): Fixed duplicate-short-description. -- Daniel Leidert (dale) Sun, 15 Feb 2009 20:54:55 +0100 xmakemol (5.16-2) experimental; urgency=low * debian/control: Vcs fields transition. The xmakemol-gl package has been downgraded to priority extra to fix a violation of section 2.5 of the Debian policy (thanks to debcheck). Added DM-Upload-Allowed. (Maintainer): Set to the debichem team address. Moved Michael to Uploaders. (Uploaders): Removed LI. Thanks for your work! (Standards-Version): Updated to 3.8.0. (Vcs-Svn): Set to experimental location. * debian/copyright: Updated. * debian/dirs: Removed (useless). * debian/docs: Ditto. * debian/xmakemol-gl.dirs: Ditto. * debian/xmakemol-gl.docs: Ditto. * debian/menu: Renamed to debian/xmakemol.menu. * debian/xmakemol.desktop: Added .desktop file based on Ubuntu version. * debian/README.Debian: Renamed to debian/xmakemol.README.Debian, updated and copied to debian/xmakemol-gl.README.Debian. * debian/rules: Rewrote some target stuff using implicit rules to reduce target sizes. (clean): Made it slightly easier. (binary-arch): Reordered calls a bit. Removed the argument to dh_installman. Install docs to all binary packages. Install .desktop files. * debian/watch: Fixed. -- Daniel Leidert (dale) Sat, 31 Jan 2009 00:53:13 +0100 xmakemol (5.16-1) unstable; urgency=low * New upstream release 5.16. [ Daniel Leidert ] * debian/control: Homepage field transition. (Uploaders): Added LI and myself. * debian/rules: Massive updates for a cleaner autotools-feature usage. * debian/watch: Added. [ LI Daobing ] * debian/control: - build depends on libglw1-mesa-dev - depends on debhelper (>= 5) - bump policy version to 3.7.2 - add homepage to description. - remove depends on dpatch * debian/rules: - lintian doesn't like "-$(MAKE) clean", see bug#325372 - do not try install ChangeLog. - remove DH_COMPAT - install /usr/bin/xmake_anim.pl as /usr/bin/xmake_anim - remove depends on dpatch * debian/patches/02_glutInit.dpatch: deleted. * debian/patches/00list: deleted. * debian/patches: deleted. * debian/compat: added. * debian/menu: update section. * debian/xmakemol-gl.menu: update section. * debian/README.Debian: explain why xmake_anim.pl is renamed. -- Daniel Leidert (dale) Mon, 24 Sep 2007 14:34:50 +0200 xmakemol (5.15-2) unstable; urgency=medium * Urgency medium due to fix for bug which severly decreases the usefulness of xmakemol-gl. * debian/patches/02_glutInit.dpatch: New patch, taken from upstream CVS: Call glutInit() before other GLUT functions; closes: #344369. * debian/patches/00list (02_glutInit): Added. * debian/control (Build-Depends): Changed libglut3-dev to freeglut3-dev; closes: #394507. -- Michael Banck Thu, 7 Dec 2006 13:44:03 +0100 xmakemol (5.15-1) unstable; urgency=low * New upstream release. * Acknowledge NMUs; closes: #346267, #337468. * debian/control (Build-Depends): Replace xlibmesa-gl-dev with libgl1-mesa-swx11-dev; closes: #379311. -- Michael Banck Tue, 25 Jul 2006 02:10:50 +0200 xmakemol (5.14-1.2) unstable; urgency=high * Non-maintainer upload. * Split xlibs-dev build-dep (Closes: #346267). -- Luk Claes Sat, 7 Jan 2006 00:28:41 +0100 xmakemol (5.14-1.1) unstable; urgency=high * Non-maintainer upload. * Update xlibmesa build-dep to xlibmesa-gl-dev (Closes: #337468). -- Luk Claes Mon, 2 Jan 2006 18:44:29 +0100 xmakemol (5.14-1) unstable; urgency=low * New upstream release. * debian/patches/01_bbox_compile_error.dpatch: Removed, applied upstream. * debian/patches/00list: Updated. * debian/rules: Make configure-stamp depend on patch-stamp instead of build-stamp. -- Michael Banck Sat, 8 Jan 2005 02:53:53 +0100 xmakemol (5.13-1) unstable; urgency=low * New upstream release - Installs all included examples now; closes: #249817 * debian/control (Build-Depends): Replace lesstif-dev with lesstif2-dev; closes: #264204 * debian/patches/01_bbox_compile_error.dpatch: New file, fixing a compile error when building without OpenGL * debian/patches/00list: New file * debian/control (Build-Depends): Added dpatch * debian/rules: Add support for dpatch -- Michael Banck Sat, 7 Aug 2004 22:17:04 +0200 xmakemol (5.12-2) unstable; urgency=low * debian/rules (binary-arch): Include all examples from the examples/ directory. Thanks to Wolfram Quester. * debian/menu (needs, section): Quote the values. Thanks to Wolfram Quester. * debian/xmakemol-gl.menu (needs, section): Likewise. -- Michael Banck Wed, 19 May 2004 20:34:23 +0200 xmakemol (5.12-1) unstable; urgency=low * New upstream release * debian/copyright: Changed download location to savannah. -- Michael Banck Mon, 22 Mar 2004 11:51:50 +0100 xmakemol (5.11-1) unstable; urgency=low * New upstream release -- Michael Banck Mon, 15 Mar 2004 22:36:24 +0100 xmakemol (5.10-2) unstable; urgency=low * debian/control (Build-Depends): Added libglut3-dev; closes: #220590. -- Michael Banck Fri, 14 Nov 2003 11:45:59 +0100 xmakemol (5.10-1) unstable; urgency=low * New upstream release -- Michael Banck Tue, 4 Nov 2003 14:15:22 +0100 xmakemol (5.09-1) unstable; urgency=low * New upstream release * debian/xmakemol.txt: Removed * debian/docs, debian/xmakemol-gl.docs: Include xmakemol.txt -- Michael Banck Sat, 13 Sep 2003 21:57:16 +0200 xmakemol (5.08-1) unstable; urgency=low * The 'Oops, forgot about that one'-release * New upstream release * debian/copyright: Updated author's email address * debian/README.debian: Updated maintainer's email address -- Michael Banck Sat, 9 Aug 2003 22:53:39 +0200 xmakemol (5.06-2) unstable; urgency=low * Moved menu entries from Math to Science section -- Michael Banck Sun, 30 Mar 2003 18:55:08 +0200 xmakemol (5.06-1) unstable; urgency=low * New upstream release * Removed Emacs-variables from debian/changelog * Bumped Standards-Version to 3.5.6.1 -- Michael Banck Thu, 12 Sep 2002 18:55:08 +0200 xmakemol (5.05-1) unstable; urgency=low * New upstream release -- Michael Banck Sun, 7 Jul 2002 20:24:42 +0200 xmakemol (5.04-1) unstable; urgency=low * New upstream release * Changed Maintainer email address * Includes xmake_anim.pl (current CVS version) in /usr/bin now and therefore Suggests: imagemagick and gifsicle -- Michael Banck Mon, 27 May 2002 16:51:11 +0200 xmakemol (5.03-2) unstable; urgency=low * xmolemol now Suggests: openbabel, which allows converting most chemical file types into .xyz so xmakemol can display them -- Michael Banck Sun, 7 Apr 2002 11:27:21 +0200 xmakemol (5.03-1) unstable; urgency=low * New upstream release -- Michael Banck Tue, 19 Feb 2002 21:38:48 +0100 xmakemol (5.02-2) unstable; urgency=low * Fixed bounding-box for .eps-export * Included fix for crash in file-select widget -- Michael Banck Fri, 21 Dec 2001 01:52:11 +0100 xmakemol (5.02-1) unstable; urgency=low * New upstream release * xmakemol can now output .fig-files and therefore Suggests: transfig * Cleaned up debian/rules a bit * Included html documentation from tarball -- Michael Banck Tue, 13 Nov 2001 01:06:18 +0100 xmakemol (5.01-2) unstable; urgency=low * Fixed long description in control file -- Michael Banck Fri, 9 Nov 2001 18:27:29 +0100 xmakemol (5.01-1) unstable; urgency=low * Initial Release; closes: #117663 * Included an updated elements-file from CVS * Added the (somewhat outdated) html-manual as .txt-file from http://vegemite.chem.nottingham.ac.uk/~xmakemol/manual/xmakemol.html -- Michael Banck Wed, 31 Oct 2001 20:18:07 +0100 debian/xmakemol.README.Debian0000644000000000000000000000065511146070204013044 0ustar xmakemol for Debian ------------------- If you want to change the /usr/share/xmakemol/elements file you should rather copy the file somewhere else and either run xmakemol from that directory or set XM_ELEMENTS to the directory or file. -- Michael Banck , 2001-10-29 xmake_anim.pl is installed as /usr/bin/xmake_anim (Debian Policy Manual, section 10.4). -- LI Daobing , 2007-09-19 debian/control0000644000000000000000000000473112211711663010576 0ustar Source: xmakemol Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: autotools-dev (>> 20100122.1~), debhelper (>> 7.0.50~), freeglut3-dev, libmotif-dev, libgl1-mesa-dev | libgl-dev, libglw1-mesa-dev, libxi-dev, libxpm-dev, libxt-dev Standards-Version: 3.9.4 Homepage: http://www.nongnu.org/xmakemol/ Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/xmakemol/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/xmakemol/ Package: xmakemol Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Suggests: gifsicle, imagemagick, openbabel, transfig Conflicts: xmakemol-gl Description: program for visualizing atomic and molecular systems XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds. . Features include: - Animating multiple frame files - Interactive measurement of bond lengths, bond angles and torsion angles - Control over atom/bond sizes - Exporting to Xpm, Encapsulated PostScript and XYZ formats - Toggling the visibility of groups of atoms - Editing the positions of subsets of atoms Package: xmakemol-gl Architecture: any Priority: extra Depends: ${misc:Depends}, ${shlibs:Depends} Suggests: gifsicle, imagemagick, openbabel, transfig Conflicts: xmakemol Description: program for visualizing atomic and molecular systems (OpenGL) XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds. . Features include: - Animating multiple frame files - Interactive measurement of bond lengths, bond angles and torsion angles - Control over atom/bond sizes - Exporting to Xpm, Encapsulated PostScript and XYZ formats - Toggling the visibility of groups of atoms - Editing the positions of subsets of atoms . This is the OpenGL-enabled XMakemol package. The images are rendered using true 3D graphics primitives, and can be exported using the Xpm format; red/blue stereo images can also be produced. The OpenGL package provides more display options, along with better support for displaying vectors. Ellipses can also be rendered. debian/compat0000644000000000000000000000000211752042436010370 0ustar 7