[med-svn] r12301 - in trunk/packages/zhanglab: . edtsurf edtsurf/trunk edtsurf/trunk/debian edtsurf/trunk/debian/patches edtsurf/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Sat Sep 29 17:49:47 UTC 2012
Author: moeller
Date: 2012-09-29 17:49:47 +0000 (Sat, 29 Sep 2012)
New Revision: 12301
Added:
trunk/packages/zhanglab/edtsurf/
trunk/packages/zhanglab/edtsurf/trunk/
trunk/packages/zhanglab/edtsurf/trunk/debian/
trunk/packages/zhanglab/edtsurf/trunk/debian/EDTSurf.1
trunk/packages/zhanglab/edtsurf/trunk/debian/README.Debian
trunk/packages/zhanglab/edtsurf/trunk/debian/README.source
trunk/packages/zhanglab/edtsurf/trunk/debian/changelog
trunk/packages/zhanglab/edtsurf/trunk/debian/compat
trunk/packages/zhanglab/edtsurf/trunk/debian/control
trunk/packages/zhanglab/edtsurf/trunk/debian/copyright
trunk/packages/zhanglab/edtsurf/trunk/debian/docs
trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.dirs
trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.install
trunk/packages/zhanglab/edtsurf/trunk/debian/manpages
trunk/packages/zhanglab/edtsurf/trunk/debian/patches/
trunk/packages/zhanglab/edtsurf/trunk/debian/patches/CFLAGS_missing_in_Makefile.patch
trunk/packages/zhanglab/edtsurf/trunk/debian/patches/series
trunk/packages/zhanglab/edtsurf/trunk/debian/rules
trunk/packages/zhanglab/edtsurf/trunk/debian/source/
trunk/packages/zhanglab/edtsurf/trunk/debian/source/format
trunk/packages/zhanglab/edtsurf/trunk/debian/upstream
Log:
Nice program, nice publication.
Property changes on: trunk/packages/zhanglab/edtsurf/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/EDTSurf.1
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/EDTSurf.1 (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/EDTSurf.1 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,30 @@
+.TH EDTSurf "1" "September 2012"
+.SH NAME
+EDTSurf \- calculation of mesh for protein surfaces
+.SH SYNOPSIS
+EDTSurf -i pdbname ...
+.SH OPTIONS
+.TP
+\fB\-i\fR pdbname ...
+.TP
+\fB\-o\fR outname
+.TP
+\fB\-t\fR 1\-MC 2\-VCMC
+.TP
+\fB\-s\fR 1\-VWS 2\-SAS 3\-MS 4\-SES
+.TP
+\fB\-c\fR 1\-pure 2\-atom 3\-chain
+.TP
+\fB\-p\fR probe radius [0,2.0]
+.TP
+\fB\-f\fR scale factor (0,20.0]
+.TP
+\fB\-h\fR 1\-in and out 2\-out 3\-in
+.TP
+output1: outname.ply
+.TP
+output2: outname.asa
+.TP
+output3: outname\-cav.pdb
+.SH "SEE ALSO"
+http://zhanglab.ccmb.med.umich.edu/EDTSurf
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/README.Debian
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/README.Debian 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,3 @@
+This package was not yet fully tested. Please send comments.
+Many thanks
+Steffen
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/README.source
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/README.source (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/README.source 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,7 @@
+edtsurf for Debian
+------------------
+
+The binary was removed from the source tree.
+
+
+
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/changelog
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/changelog (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/changelog 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,5 @@
+edtsurf (0.2009-1) unstable; urgency=low
+
+ * Initial release (Closes: #689163)
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 29 Sep 2012 16:54:15 +0200
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/compat
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/compat (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/compat 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+8
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/control
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/control (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/control 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,20 @@
+Source: edtsurf
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), dpkg-dev (>= 1.16.1~)
+Standards-Version: 3.9.4
+Homepage: http://zhanglab.ccmb.med.umich.edu/EDTSurf/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/edtsurf/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/edtsurf/trunk/
+
+Package: edtsurf
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: meshlab
+Description: triangulated mesh surfaces for protein structures
+ EDTSurf is a open source program to construct triangulated surfaces
+ for macromolecules. It generates three major macromolecular surfaces:
+ van der Waals surface, solvent-accessible surface and molecular surface
+ (solvent-excluded surface). EDTsurf also identifies cavities which are
+ inside of macromolecules.
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/copyright
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/copyright (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/copyright 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: edtsurf
+Source: http://zhanglab.ccmb.med.umich.edu/EDTSurf
+
+Files: *
+Copyright: 2009 Dong Xu and Yang Zhang <zhng at umich.edu>
+License:
+ Permission to use, copy, modify, and distribute this program for
+ any purpose, with or without fee, is hereby granted, provided that
+ the notices on the head, the reference information, and this
+ copyright notice appear in all copies or substantial portions of
+ the Software. It is provided "as is" without express or implied
+ warranty.
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+License: GPL-2+
+ This package 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 package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/docs
===================================================================
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.dirs
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.dirs (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.dirs 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.install
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.install (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/edtsurf.install 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+EDTSurf usr/bin
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/manpages
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/manpages (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/manpages 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+debian/EDTSurf.1
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/patches/CFLAGS_missing_in_Makefile.patch
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/patches/CFLAGS_missing_in_Makefile.patch (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/patches/CFLAGS_missing_in_Makefile.patch 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,19 @@
+Index: edtsurf-0.2009/Makefile
+===================================================================
+--- edtsurf-0.2009.orig/Makefile
++++ edtsurf-0.2009/Makefile
+@@ -1,9 +1,9 @@
+ EDTSurf : ParsePDB.o ProteinSurface.o EDTSurf.o
+- g++ ParsePDB.o ProteinSurface.o EDTSurf.o -o EDTSurf
++ g++ $(LDFLAGS) ParsePDB.o ProteinSurface.o EDTSurf.o -o EDTSurf
+ rm *.o
+ ProteinSurface.o : ProteinSurface.cpp
+- g++ -c ProteinSurface.cpp -o ProteinSurface.o
++ g++ $(CPPFLAGS) $(CXXFLAGS) -c ProteinSurface.cpp -o ProteinSurface.o
+ ParsePDB.o : ParsePDB.cpp
+- g++ -c ParsePDB.cpp -o ParsePDB.o
++ g++ $(CPPFLAGS) $(CXXFLAGS) -c ParsePDB.cpp -o ParsePDB.o
+ EDTSurf.o : EDTSurf.cpp
+- g++ -c EDTSurf.cpp -o EDTSurf.o
+\ No newline at end of file
++ g++ $(CPPFLAGS) $(CXXFLAGS) -c EDTSurf.cpp -o EDTSurf.o
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/patches/series
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/patches/series (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/patches/series 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+CFLAGS_missing_in_Makefile.patch
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/rules
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/rules (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/rules 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+format,+bindnow
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
+
+%:
+ dh $@
+
+override_dh_clean:
+ dh_clean
+ rm -f EDTSurf
Property changes on: trunk/packages/zhanglab/edtsurf/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/source/format
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/source/format (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/source/format 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/zhanglab/edtsurf/trunk/debian/upstream
===================================================================
--- trunk/packages/zhanglab/edtsurf/trunk/debian/upstream (rev 0)
+++ trunk/packages/zhanglab/edtsurf/trunk/debian/upstream 2012-09-29 17:49:47 UTC (rev 12301)
@@ -0,0 +1,14 @@
+Contact: Yang Zhang <zhng at umich.edu>
+Homepage: http://zhanglab.ccmb.med.umich.edu/EDTSurf/
+Name: EDTSurf
+Reference:
+ AUTHOR: Dong Xu and Yang Zhang
+ TITLE:
+ Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
+ JOURNAL: PLoS ONE
+ YEAR: 2009
+ PAGES: e8140
+ VOLUME: 4
+ NUMBER: 12
+ eprint: http://zhanglab.ccmb.med.umich.edu/EDTSurf/EDTSurf.pdf
+ DOI: 10.1371/journal.pone.0008140
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