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C..f s. O O . . ", " o o . O O k H.].H.G.D.j.j.j.p * 2 ) L.b.c.^ l.m.m.v.0.:.u = + ", " . O o . 5 5XpXwX7X1X2X].].i.- X X * & , g R M.m.n.nXLXAXzX8X", "8.&.< o $ -XFXZXVXbXfXsXiXwXw.* X X . 6 hXjX}.MXIXIXIXIX", "JXBXyXk.7.zXDXFXCXBXBXbXcXtX&.X X X . 5 xXKXJXHXKXKXKXKX", "e e e r = ; e r q q q q q = o q e e e e e e e ", "YXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYX", "YXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYX", "YXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYXYX" }; debian/gausssum.install0000644000000000000000000000012512112147222012415 0ustar debian/gausssum.xpm usr/share/pixmaps debian/gausssum.desktop usr/share/applications debian/watch0000644000000000000000000000007510641772521010226 0ustar version=3 http://sf.net/gausssum/GaussSum-([\d\.]+)\.tar\.gz debian/control0000644000000000000000000000227612112153535010576 0ustar Source: gausssum Section: science Priority: optional Maintainer: Debichem Team Uploaders: Daniel Leidert (dale) , Michael Banck Standards-Version: 3.9.3 Build-Depends: debhelper (>> 7.0.50~), python (>> 2.6.6-3~) Build-Depends-Indep: tofrodos X-Python-Version: current Homepage: http://gausssum.sourceforge.net Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/gausssum/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/gausssum/ DM-Upload-Allowed: yes Package: gausssum Architecture: all Depends: gnuplot, python-cclib, python-imaging-tk, python-numpy, python-tk, ${misc:Depends}, ${python:Depends} Description: parse and display Gaussian, GAMESS, and etc's output GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information. . GaussSum uses GNUPlot to display the progress of geometry optimisations, density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra, and electron density difference maps. It can also display all lines containing an arbitrary phrase and more. debian/source/0000755000000000000000000000000012112147222010460 5ustar debian/source/format0000644000000000000000000000001412112147222011666 0ustar 3.0 (quilt) debian/gausssum.10000644000000000000000000000452012112147222011112 0ustar .TH "GAUSSSUM" "1" "February 15, 2008" .SH NAME gausssum \- parses the output of a Gaussian, GAMESS or HyperChem job .SH SYNOPSIS .B gausssum .RI [ filename ] .SH DESCRIPTION .B gausssum parses the output file of a Gaussian, GAMESS or HyperChem computational chemistry job to extract useful information. It uses .BR gnuplot (1) to graphically display of the output. GaussSum can do the following: (Gau=Gaussian, GAM=GAMESS, Hyp=HyperChem) .IP \(bu display all lines containing a certain phrase (any) .IP \(bu follow the progress of the SCF convergence (Gau,GAM) .IP \(bu follow the progress of a geometry optimisation (Gau,GAM) .IP \(bu extract molecular orbital information, including contributions of groups of atoms to the molecular orbitals (Gau,GAM) .IP \(bu plot the density of states spectrum (and the partial density of states, in the case of groups of atoms) (Gau,GAM) .IP \(bu plot the crystal orbital overlap population (COOP) spectrum, which gives information on the bonding/anti\-bonding nature of an overlap between atoms/groups (Gau,GAM) .IP \(bu extract information on the UV\-Vis transitions (Gau,Hyp), including the change in the charge density of groups of atoms (Gau) .IP \(bu plot the UV\-Vis spectrum (Gau,Hyp) and the circular dichroism spectrum (Gau) .IP \(bu automate the creation of electron density difference maps, which visually show the change in charge density associated with a given electronic transition (Gau) .IP \(bu extract information on IR (Gau,GAM) and Raman vibrations (Gau) .IP \(bu plot the IR and Raman spectra, which may be scaled using general or individual scaling factors (Gau) .SH "CITATION" If you use GaussSum to obtain results for publication, please cite it as follows: .IP .B N. M. O'Boyle, A. L. Tenderholt and K. M. Langner. J. Comp. Chem. 2008, 29, .B 839-845. .SH "SEE ALSO" .BR gnuplot (1) .PP \fI/usr/share/doc/gausssum/html/\fR (or equivalent on your system) .SH AUTHOR This manual page was written by \fBJordan Mantha\fR <\&mantha@ubuntu\.com\&> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. .PP On Debian systems, the complete text of the GNU General Public License can be found in \fI/usr/share/common\-licenses/GPL\fR. debian/changelog0000644000000000000000000002353312117453026011047 0ustar gausssum (2.2.6.1-1) unstable; urgency=low * New upstream point release. -- Michael Banck Mon, 11 Mar 2013 23:09:23 +0100 gausssum (2.2.6-1) unstable; urgency=low * New upstream release. [ Daniel Leidert (dale) ] * debian/control (Build-Depends): Fixed python version. * debian/upstream (Author): Minor fix. [ Michael Banck ] * debian/patches/debian_cclib.patch: No longer needed hunk removed. * debian/patches/debian_paths.patch: Refreshed. * debian/control (Uploaders): Added myself. -- Michael Banck Sat, 23 Feb 2013 15:56:55 +0100 gausssum (2.2.5-2) unstable; urgency=low * debian/compat: Increased dh compatibility level to 7. * debian/control: Added X-Python-Version field. (Standards-Version): Bumped to 3.9.3. (Build-Depends): Dropped dpatch. Increased required debhelper version. (Build-Depends-Indep): Dropped python-support. (Depends): Added python-cclib. * debian/copyright: Use versioned symlinks. * debian/gausssum.1: Fixed citation section. * debian/gausssum.desktop (Icon): Use full path according to spec. * debian/gausssum.manpages: Added. * debian/rules: Rewritten for debhelper 7. * debian/setup.py: Don't copy nor install internal cclib. * debian/upstream: Added. * debian/README.source: Dropped obsolete file. * debian/patches/debian_paths.dpatch: Renamed to debian/patches/debian_paths.patch. * debian/patches/debian_cclib.patch: Added. - Use python-cclib instead of the internal copy. * debian/patches/00list: Renamed to debian/patches/series and adjusted. * debian/source/format: Added for quilt-based format 3.0 (closes: #664303). -- Daniel Leidert (dale) Tue, 01 May 2012 23:46:49 +0200 gausssum (2.2.5-1) unstable; urgency=low * New upstream release. * debian/control (Vcs-Browser): Point to real location. -- Daniel Leidert (dale) Mon, 07 Feb 2011 07:52:01 +0100 gausssum (2.2.4-1) unstable; urgency=low * New upstream release. * debian/control (Standards-Version): Bumped to 3.9.1. -- Daniel Leidert (dale) Sun, 01 Aug 2010 22:19:47 +0200 gausssum (2.2.3-1) unstable; urgency=low * New upstream release. * debian/control (Standards-Version): Bumped to 3.8.4. (Build-Depends): Fixed build-depends-on-python-dev-with-no-arch-any by replacing python-dev by python. (Depends): Fixed debhelper-but-no-misc-depends. -- Daniel Leidert (dale) Mon, 22 Feb 2010 23:57:02 +0100 gausssum (2.2.2-1) unstable; urgency=low * New upstream release. - Uses hidden user directories now. * debian/patches/debian_paths.dpatch: Adjusted. gnuplot location patch is obsolete by new code in gausssum/gausssumgui.py. * debian/patches/fix_startup_exception.dpatch: Dropped (applied upstream). * debian/patches/00list: Adjusted. -- Daniel Leidert (dale) Wed, 25 Nov 2009 00:16:05 +0100 gausssum (2.2.0-1) unstable; urgency=low * New upstream release. * debian/control (Standards-Version): Bumped to 3.8.3. * debian/rules (install): Use /usr/share/python/python.mk and pass --install-layout=deb to be safe. (binary-indep): Drop deprecated dh_desktop. * debian/patches/fix_startup_exception.dpatch: Added. - Fix 'ImportError: No module named cclib.data' startup error. * debian/patches/00list: Adjusted. -- Daniel Leidert (dale) Mon, 16 Nov 2009 03:10:54 +0100 gausssum (2.1.6-1) unstable; urgency=low * New upstream release 2.1.6. * debian/control (Standards-Version): Bumped to 3.8.1. * debian/copyright: Updated and fixed (thanks to Noel for clarification of the licenses). -- Daniel Leidert (dale) Mon, 06 Apr 2009 13:21:12 +0200 gausssum (2.1.5-1) unstable; urgency=low * New upstream release 2.1.5. [ Daniel Leidert ] * debian/control: Added DM-Upload-Allowed. (Standards-Version): Updated to 3.8.0. (Uploaders): Removed LI as requested. Thanks for your work! Added myself. * debian/copyright: Updated. Added cclib copyright and license information. * debian/doc-base (Section): Fixed accordingly to version 0.8.10 of the doc-base manual. Renamed to debian/gausssum.doc-base. * debian/install: Removed Docs/*. Renamed to debian/gausssum.install. * debian/menu: Renamed to debian/gausssum.menu. * debian/gausssum.1: Updated/improved. Added citation information. * debian/rules: Create a setup.py with the current upstream version. Cleaned the file a bit. (binary-indep): Install the HTML changelog. * debian/setup.py: Improved a bit. Also install documentation from here. Added automatically replaced upstream version information and homepage. * debian/README.Debian: Dropped. Changelog is installed as changelog.html.gz/changelog.gz. Added citation information to gausssum.1. * debian/README.source: Added for policy compatibility. * debian/patches/debian_paths.dpatch: Added. Merge all Debian specific path changes into this patch. * debian/patches/06_image_path.dpatch: Merged to debian_paths.dpatch. * debian/patches/07_html_path.dpatch: Ditto. * debian/patches/00list: Adjusted. [ LI Daobing ] * debian/gausssum.desktop: fix lintian info: desktop-entry-contains-encoding-key -- Daniel Leidert (dale) Sat, 28 Feb 2009 22:06:35 +0100 gausssum (2.1.4-1) unstable; urgency=low * New upstream release. * debian/README.Debian: update citation file name. -- LI Daobing Tue, 13 Nov 2007 03:58:10 +0800 gausssum (2.1.3-1) unstable; urgency=low * New upstream release 2.1.3. -- LI Daobing Tue, 23 Oct 2007 20:36:08 +0800 gausssum (2.1.2-1) unstable; urgency=low * New upstream release 2.1.2. * New maintainer. [ LI Daobing ] * menu: update section. [ Daniel Leidert ] * debian/control: Homepage field transition. XS-Vcs-* fields transition. -- LI Daobing Fri, 05 Oct 2007 00:08:39 +0000 gausssum (2.1.1-1) unstable; urgency=low * debian/gausssum.install: move to install * debian/gausssum.doc-base: move to doc-base * debian/gausssum.menu: move to menu * debian/gausssum.manpages: use debian/rules as there is only 1 man page * debian/control: remove LI Daobing as Uploader for now [ LI Daobing ] * new upstream release. -- Jordan Mantha Sun, 05 Aug 2007 22:34:05 -0700 gausssum (2.1.0-1) unstable; urgency=low [ LI Daobing ] * new upstream release. * control: depends on python-numpy. * gausssum.doc-base: remove trailing blank to clear lintian warning. * patches/07_html_path.dpatch: added. * patches/00list: updated. [ Daniel Leidert ] * debian/watch: Slightly updated. -- LI Daobing Sat, 30 Jun 2007 21:49:17 +0800 gausssum (2.0.5-1~dev) unstable; urgency=low * New upstream release. -- LI Daobing Wed, 02 May 2007 23:00:44 +0800 gausssum (2.0.4-1) unreleased; urgency=low * New upstream release 2.0.4 (closes: #384963, #402893) [ LI Daobing ] * update debian policy to 3.7.2 * remove 05_gausssum_py.dpatch * add 06_image_path.dpatch * use dh_pysupport instead of dh_python * update setup.py * add debian/watch * debian/control: depends on tofrodos instead of sysutils (closes: #382169) [ Daniel Leidert ] * debian/control (Uploaders): Added LI Daobing. (Build-Depends, Build-Depends-Indep): Fixed (accordingly to section 7.6 of the policy). (Description): Improved wording in short description and changed to standard Homepage field. * debian/dirs: Removed (useless with dh_install). * debian/gausssum.desktop: Added MimeType field to register gaussum for the file formats it can read (maybe incomplete). (Categories): Fixed invalid field entry. * debian/gausssum.install: Added. Obsoletes the manual installation in debian/rules. * debian/menu: Renamed to gausssum.menu. * debian/rules: Removed targets already defined in dpatch.make. Changed to use dh_install to install files. Removed useless dh_installexamples call. -- LI Daobing Tue, 10 Apr 2007 20:12:43 +0800 gausssum (1.0.4-1) unstable; urgency=low * New upstream release - Bug fix for wrong symmetry labels in unrestricted calclations * Added watch file * Moved to new Debian Python Policy (Closes: Bug #380805) - added XS-Python-Version: current, >= 2.3 - added python-central support - use /usr/bin/python rather than /usr/bin/python2.3 in GaussSum.py -- Jordan Mantha Sat, 29 Jul 2006 17:23:10 -0700 gausssum (1.0.3-2) unstable; urgency=low * Modified GaussSum.py to look for python2.3 * Fixed spelling error in description (Closes: #363601) -- Jordan Mantha Mon, 3 Apr 2006 07:24:26 -0700 gausssum (1.0.3-1) unstable; urgency=low * New upstream release - Bug fixes for CD spectra calculations * Moved to dpatch for source patches -- Jordan Mantha Sat, 18 Feb 2006 22:18:36 +0000 gausssum (1.0.2-2) unstable; urgency=low * Took over ITP for LI Daobing (closes: #324632) - cleaned up debian/rules - added .desktop file - added man page -- Jordan Mantha Tue, 17 Jan 2006 14:15:29 -0800 gausssum (1.0.2-1) unstable; urgency=low * New upstream release -- LI Daobing Wed, 2 Nov 2005 16:34:57 +0800 gausssum (1.0-1) unstable; urgency=low * New upstream release * debian/menu: fix format * debian/copyright: update fsf address -- LI Daobing Fri, 7 Oct 2005 10:55:59 +0800 gausssum (0.9-1) unstable; urgency=low * New upstream release * change Standards-Version to 3.6.2 -- LI Daobing Tue, 23 Aug 2005 15:59:59 +0800 gausssum (0.8-1) unstable; urgency=low * Initial Release. -- Li Daobing Mon, 17 Jan 2005 19:46:32 +0800 debian/copyright0000644000000000000000000000241512112147222011115 0ustar This package was debianized by Li Daobing on Mon, 17 Jan 2005 19:46:32 +0800. It is currently maintained by the debichem team . It was downloaded from: http://gausssum.sourceforge.net/ Copyright Holder: **/* Copyright (C) 2005-2009 Noel O'Boyle License: GPLv2+ gausssum is licensed under the GPL version 2 or later. On Debian systems, the complete text of the GNU General Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. ============================================================================== Copyright Holder: gausssum/cclib/** Copyright (C) 2007, the cclib development team License: LGPLv2+ cclib is licensed under the LGPL version 2 or later. On Debian systems, the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL-2'. ============================================================================== The Debian packaging is Copyright (C) 2006-2009 by LI Daobing Copyright (C) 2006-2012 debichem team and is licensed under the GNU General Public License v2 or later; see also `/usr/share/common-licenses/GPL-2'. debian/compat0000644000000000000000000000000212112147222010356 0ustar 7 debian/gausssum.manpages0000644000000000000000000000002212112147222012536 0ustar debian/gausssum.1 debian/gausssum.doc-base0000644000000000000000000000045612112147222012433 0ustar Document: gausssum Title: GaussSum Manual Author: Noel O'Boyle Abstract: Manual for GaussSum, a program that parses and displays Gaussian, GAMESS, and HyperChem output. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/gausssum/html/index.html Files: /usr/share/doc/gausssum/html/*.html debian/patches/0000755000000000000000000000000012112150633010607 5ustar debian/patches/series0000644000000000000000000000004612112147222012024 0ustar debian_cclib.patch debian_paths.patch debian/patches/debian_cclib.patch0000644000000000000000000000314412112150622014206 0ustar Author: Daniel Leidert Description: Debian ships cclib in an own package. So use this one. --- a/gausssum/aboutbox.py +++ b/gausssum/aboutbox.py @@ -21,7 +21,7 @@ import copy # For deepcopy...until I find a better way of doing this import ConfigParser # For writing the settings to an .ini file -from gausssum.cclib.parser import ADF, GAMESS, Gaussian +from cclib.parser import ADF, GAMESS, Gaussian import os, sys if hasattr(sys, "frozen"): # i.e. if using py2exe installlocation = os.path.dirname(sys.executable) --- a/gausssum/electrontrans.py +++ b/gausssum/electrontrans.py @@ -20,7 +20,7 @@ import glob from gausssum.utils import GaussianSpectrum, levelname, percent -from gausssum.cclib.parser.utils import convertor +from cclib.parser.utils import convertor from Tkinter import * from gnupy import Gnuplot --- a/gausssum/gausssumgui.py +++ b/gausssum/gausssumgui.py @@ -23,7 +23,7 @@ import logging import glob -from gausssum.cclib.parser import ADF, GAMESS, Gaussian, ccopen +from cclib.parser import ADF, GAMESS, Gaussian, ccopen from gausssum.preferencesbox import PreferencesPopupBox from gausssum.aboutbox import AboutPopupBox from gausssum.popanalysis import Popanalysis --- a/gausssum/utils.py +++ b/gausssum/utils.py @@ -21,7 +21,7 @@ import copy # For deepcopy...until I find a better way of doing this import ConfigParser # For writing the settings to an .ini file -from gausssum.cclib.parser.utils import PeriodicTable +from cclib.parser.utils import PeriodicTable # from cclib.parser.utils import PeriodicTable import numpy debian/patches/debian_paths.patch0000755000000000000000000000356712112150633014267 0ustar Author: LI Daobing Description: Fix the path to the images and HTML documentation that follows the FHS in our Debian package. @DPATCH@ Index: gausssum-2.2.6/gausssum/aboutbox.py =================================================================== --- gausssum-2.2.6.orig/gausssum/aboutbox.py 2013-02-23 15:26:28.298200526 +0100 +++ gausssum-2.2.6/gausssum/aboutbox.py 2013-02-23 15:26:30.706205284 +0100 @@ -63,7 +63,7 @@ self.canvas2 = Canvas(master,width=340,height=260) self.canvas2.pack(side=TOP) - self.photo2 = PhotoImage(file=os.path.join(installlocation,"mesh.gif")) + self.photo2 = PhotoImage(file=os.path.join('/usr/share/gausssum',"mesh.gif")) self.item2 = self.canvas2.create_image(11,11,anchor=NW,image=self.photo2) Label(master,text="(c) 2009 Noel O'Boyle").pack(side=TOP) Index: gausssum-2.2.6/gausssum/gausssumgui.py =================================================================== --- gausssum-2.2.6.orig/gausssum/gausssumgui.py 2013-02-23 15:26:28.302206065 +0100 +++ gausssum-2.2.6/gausssum/gausssumgui.py 2013-02-23 15:26:30.710205235 +0100 @@ -102,7 +102,7 @@ self.frame5=Frame(self.frame1) self.frame5.pack(side=LEFT) - self.photo = PhotoImage(file=os.path.join(installlocation,"mesh2.gif")) # Doesn't work if don't use self. + self.photo = PhotoImage(file=os.path.join('/usr/share/gausssum',"mesh2.gif")) # Doesn't work if don't use self. Button(self.frame5,image=self.photo,command=self.runscript).pack(side=LEFT) self.root.bind("", self.runscript) @@ -609,6 +609,6 @@ self.saveprefs() # Save the inital settings file def webdocs(self): - webbrowser.open(os.path.join(installlocation,"..","Docs","index.html")) + webbrowser.open(os.path.join("/usr/share/doc/gausssum/html/index.html")) debian/setup.py0000644000000000000000000000104312112147222010670 0ustar from distutils.core import setup import glob setup( name = 'GaussSum', version = '@DEB_UPSTREAM_VERSION@', author = "Noel O'Boyle", author_email = "baoilleach@gmail.com", maintainer = "debichem team", maintainer_email = "debichem-devel@lists.alioth.debian.org", url = "http://gausssum.sf.net", license = "GNU GPL", scripts = ['GaussSum.py'], packages = ['gausssum'], package_dir = {'gausssum': 'gausssum'}, data_files = [ ('share/gausssum', ['mesh2.gif', 'mesh.gif']), ('share/doc/gausssum/html', glob.glob('Docs/*')) ] ) debian/rules0000755000000000000000000000134012112147222010236 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 PACKAGE = gausssum DEB_UPSTREAM_VERSION = $(shell dpkg-parsechangelog | sed -n -e 's/^Version: \(.*\)-[^-]*$$/\1/p') %: dh $@ --with=python2 --buildsystem=python_distutils --parallel setup.py: debian/setup.py sed -e "s/@DEB_UPSTREAM_VERSION@/$(DEB_UPSTREAM_VERSION)/g" < $< > $@ override_dh_auto_clean: setup.py dh_auto_clean override_dh_auto_build: setup.py dh_auto_build override_dh_auto_install: setup.py dh_auto_install mv $(CURDIR)/debian/$(PACKAGE)/usr/bin/GaussSum.py $(CURDIR)/debian/$(PACKAGE)/usr/bin/gausssum fromdos $(CURDIR)/debian/$(PACKAGE)/usr/bin/gausssum override_dh_clean: dh_clean setup.py override_dh_installchangelogs: dh_installchangelogs Docs/pr01.html debian/upstream0000644000000000000000000000055712112147222010752 0ustar Name: GaussSum Reference: - Author: Noel M. O'Boyle and Adam L. Tenderholt and Karol M. Langner Title: "cclib: A library for package-independent computational chemistry algorithms" Journal: J. Comp. Chem. Year: 2008 Volume: 29 Number: 5 Pages: 839-845 URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20823/abstract DOI: 10.1002/jcc.20823