[med-svn] r1061 - in trunk/packages/solvate/trunk: . debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Tue Jan 1 22:52:32 UTC 2008
Author: smoe-guest
Date: 2008-01-01 22:52:32 +0000 (Tue, 01 Jan 2008)
New Revision: 1061
Added:
trunk/packages/solvate/trunk/debian/
trunk/packages/solvate/trunk/debian/README.Debian
trunk/packages/solvate/trunk/debian/README.Debian.source
trunk/packages/solvate/trunk/debian/changelog
trunk/packages/solvate/trunk/debian/compat
trunk/packages/solvate/trunk/debian/control
trunk/packages/solvate/trunk/debian/copyright
trunk/packages/solvate/trunk/debian/manpages
trunk/packages/solvate/trunk/debian/rules
trunk/packages/solvate/trunk/debian/solvate-doc.dirs
trunk/packages/solvate/trunk/debian/solvate-doc.doc-base
trunk/packages/solvate/trunk/debian/solvate-doc.docs
trunk/packages/solvate/trunk/debian/solvate-doc.install
trunk/packages/solvate/trunk/debian/solvate.1
trunk/packages/solvate/trunk/debian/solvate.dirs
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/solvate/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/solvate/trunk/debian/README.Debian
===================================================================
--- trunk/packages/solvate/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/solvate/trunk/debian/README.Debian 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,6 @@
+solvate for Debian
+------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 28 Dec 2007 01:45:03 +0100
Added: trunk/packages/solvate/trunk/debian/README.Debian.source
===================================================================
--- trunk/packages/solvate/trunk/debian/README.Debian.source (rev 0)
+++ trunk/packages/solvate/trunk/debian/README.Debian.source 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,10 @@
+solvate for Debian
+------------------
+
+The original source file contained a file docu.ps that was obviously
+prepared from the HTML documentation that is provided. I refrained from
+transforming all the gifs to pngs.
+
+Steffen
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 28 Dec 2007 01:45:03 +0100
Added: trunk/packages/solvate/trunk/debian/changelog
===================================================================
--- trunk/packages/solvate/trunk/debian/changelog (rev 0)
+++ trunk/packages/solvate/trunk/debian/changelog 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,6 @@
+solvate (1.0-1) unstable; urgency=low
+
+ * Initial release.
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 28 Dec 2007 01:45:03 +0100
+
Added: trunk/packages/solvate/trunk/debian/compat
===================================================================
--- trunk/packages/solvate/trunk/debian/compat (rev 0)
+++ trunk/packages/solvate/trunk/debian/compat 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1 @@
+5
Added: trunk/packages/solvate/trunk/debian/control
===================================================================
--- trunk/packages/solvate/trunk/debian/control (rev 0)
+++ trunk/packages/solvate/trunk/debian/control 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,23 @@
+Source: solvate
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 5)
+Standards-Version: 3.7.2
+Homepage: http://www.mpibpc.mpg.de/groups/grubmueller/start/index.html
+
+Package: solvate
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: sets water molecules around protein structures
+ For molecular dynamics simulations it is sometimes appropriate
+ not to model in the vacuum but to have the proteins surrounded
+ by their solvent. This program computes the location of water
+ molecules such that the resulting PDB files become suitable
+ for further analyses.
+
+Package: solvate-doc
+Architecture: all
+Description: Documentation for solvate
+ HTML documentation for solvate, the tool to prepare
+ water cubes around proteins.
Added: trunk/packages/solvate/trunk/debian/copyright
===================================================================
--- trunk/packages/solvate/trunk/debian/copyright (rev 0)
+++ trunk/packages/solvate/trunk/debian/copyright 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,68 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on
+Fri, 28 Dec 2007 01:45:03 +0100.
+
+It was downloaded from http://www.mpibpc.mpg.de/groups/grubmueller/start/index.html
+
+Upstream Author:
+
+ Helmut Grubmueller <hgrubmu at gwdg.de>
+
+Copyright:
+
+ Helmut Grubmueller 1996
+
+License:
+
+ General License Agreement and Lack of Warranty
+
+ This software is distributed in the hope that it will be useful but
+ without any warranty. The author does not accept responsibility to
+ anyone for the consequences of using it or for whether it serves
+ any particular purpose or works at all. No warranty is made about
+ the software or its performance.
+
+ Use and copying of this software and the preparation of derivative
+ works based on this software are permitted, so long as the following
+ conditions are met:
+
+ The copyright notice and this entire notice are included intact and
+ prominently carried on all copies and supporting documentation.
+
+ No fees or compensation are charged for use, copies, or access to
+ this software. You may charge a nominal distribution fee for the
+ physical act of transferring a copy, but you may not charge for the
+ program itself.
+
+ If you modify this software, you must cause the modified file(s)
+ to carry prominent notices describing the changes, who made the
+ changes, and the date of those changes. Please do inform the author
+ about major modifications.
+
+ Any work distributed or published that in whole or in part contains
+ or is a derivative of this software or any part thereof is subject
+ to the terms of this agreement. The aggregation of another unrelated
+ program with this software or its derivative on a volume of storage
+ or distribution medium does not bring the other program under the
+ scope of these terms.
+
+ This software is made available as is, and is distributed without
+ warranty of any kind, either expressed or implied. In no event
+ will the author or his institutions be liable to you for damages,
+ including lost profits, lost monies, or other special, incidental or
+ consequential damages arising out of or in connection with the use
+ or inability to use (including but not limited to loss of data or
+ data being rendered inaccurate or losses sustained by third parties
+ or a failure of the program to operate as documented) the program,
+ even if you have been advised of the possibility of such damages, or
+ for any claim by any other party, whether in an action of contract,
+ negligence, or other tortuous action.
+
+ SOLVATE is written by Helmut Grubmüller, Theoretical
+ Biophysics Group, Institut für Medizinische Optik,
+ Ludwig-Maximilians-Universität München, München, Germany. Copyright
+ © 1996. All rights reserved.
+
+
+The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/solvate/trunk/debian/manpages
===================================================================
--- trunk/packages/solvate/trunk/debian/manpages (rev 0)
+++ trunk/packages/solvate/trunk/debian/manpages 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1 @@
+debian/solvate.1
Added: trunk/packages/solvate/trunk/debian/rules
===================================================================
--- trunk/packages/solvate/trunk/debian/rules (rev 0)
+++ trunk/packages/solvate/trunk/debian/rules 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,83 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+#
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets by Bill Allombert 2001
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+CFLAGS=-O2
+
+#Architecture
+build: build-arch build-indep
+
+build-arch: build-arch-stamp
+build-arch-stamp:
+ # equivalent to upstream's Makefiles
+ gcc $(CFLAGS) -o solvate solvate.c -lm
+ touch $@
+
+build-indep: build-indep-stamp
+build-indep-stamp:
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-arch-stamp build-indep-stamp configure-stamp
+ dh_clean solvate
+
+install: install-indep install-arch
+install-indep:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -i
+ dh_installdirs -i
+ dh_install -i
+ # in debian/solvate-doc.docs
+ #cp *.pdb *.psf $(CURDIR)/debian/solvate/usr/share/doc/solvate-doc/
+
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -s
+ dh_installdirs -s
+ cp solvate $(CURDIR)/debian/solvate/usr/bin/
+
+ dh_install -s
+
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary-indep: build-indep install-indep
+ $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+binary-arch: build-arch install-arch
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
Property changes on: trunk/packages/solvate/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/solvate/trunk/debian/solvate-doc.dirs
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate-doc.dirs (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate-doc.dirs 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1 @@
+usr/share/doc/solvate-doc/
Added: trunk/packages/solvate/trunk/debian/solvate-doc.doc-base
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate-doc.doc-base (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate-doc.doc-base 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,9 @@
+Document: solvate
+Title: Manual to Solvate
+Author: Helmut Grubmueller
+Abstract: Complete usage instructions for solvate
+Section: Science
+
+Format: HTML
+Index: /usr/share/doc/solvate/docu_html/index.html
+Files: /usr/share/doc/solvate/docu_html/*.html /usr/share/doc/solvate/docu_html/*.gif
Added: trunk/packages/solvate/trunk/debian/solvate-doc.docs
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate-doc.docs (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate-doc.docs 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,5 @@
+docu_html
+bpti.pdb
+globh.pdb
+bpti.psf
+globh.psf
Added: trunk/packages/solvate/trunk/debian/solvate-doc.install
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate-doc.install (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate-doc.install 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,2 @@
+#DOCS#
+
Added: trunk/packages/solvate/trunk/debian/solvate.1
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate.1 (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate.1 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1,82 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH SOLVATE 1 "Dezember 28, 2007"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+solvate \- surround protein with water molecules
+.SH SYNOPSIS
+.B solvate
+.RI [-t thick] [-r radius] [-n ngauss] [-ug] [-ub]
+ [-s] [-v] [-bulk] [-w] [-ion] [-psf] [infile] outfile
+.SH DESCRIPTION
+SOLVATE prepares of a water shell around solutes.
+
+.B solvate
+command.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+\" respectively.
+.SH OPTIONS
+A summary of options is included below.
+.TP
+.B \-t thick
+minimum water shell thickness in Angstrom (default: 10.0)
+.TP
+.B \-r radius
+maximum boundary curvature radius in Angstrom (default: 100000.0)
+.TP
+.B \-n ngauss
+use ngauss gaussians to define solvant boundary (default: 1)
+.TP
+.B \-s
+write surface statistics to file surface_stat.
+.TP
+.B \-v
+write volume statistics to file volume_stat.
+.TP
+.B \-ug
+use gaussians from file gaussians (skip gaussian learning phase).
+.TP
+.B \-ub
+use boundary definition from file boundary (skip gaussian learning phase and boundary adjustment).
+.TP
+.B \-bulk
+output only bulk water (i.e., no buried water molecules)
+.TP
+.B \-w
+output only water molecules (i.e., not the solute)
+.TP
+.B \-ion
+add ions (na+/cl-) in isotonic/Debye-Hueckel concentration
+.TP
+.B \-psf
+output XPLOR-script mkpsf.inp for generating a psf-file
+.TP
+.RI infile
+pdb-file (no extension) of solute (if omitted, a water droplet is created)
+.TP
+.RI outfile
+pdb-file (no extension) of water shell
+
+.SH SEE ALSO
+
+.SH AUTHOR
+SOLVATE was written 1996 by Helmut Grubmueller
+
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (but may be used by others).
Added: trunk/packages/solvate/trunk/debian/solvate.dirs
===================================================================
--- trunk/packages/solvate/trunk/debian/solvate.dirs (rev 0)
+++ trunk/packages/solvate/trunk/debian/solvate.dirs 2008-01-01 22:52:32 UTC (rev 1061)
@@ -0,0 +1 @@
+usr/bin
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