[med-svn] r1261 - in trunk/packages/autodocksuite/trunk/debian: . patches
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Sat Feb 2 13:57:13 UTC 2008
Author: smoe-guest
Date: 2008-02-02 13:57:12 +0000 (Sat, 02 Feb 2008)
New Revision: 1261
Added:
trunk/packages/autodocksuite/trunk/debian/patches/
trunk/packages/autodocksuite/trunk/debian/patches/addHelp.patch
trunk/packages/autodocksuite/trunk/debian/patches/series
Modified:
trunk/packages/autodocksuite/trunk/debian/README.Debian
trunk/packages/autodocksuite/trunk/debian/autodock4.1
trunk/packages/autodocksuite/trunk/debian/autogrid4.1
trunk/packages/autodocksuite/trunk/debian/control
trunk/packages/autodocksuite/trunk/debian/rules
Log:
Further improvements made for the man pages.
Modified: trunk/packages/autodocksuite/trunk/debian/README.Debian
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/README.Debian 2008-02-02 12:19:10 UTC (rev 1260)
+++ trunk/packages/autodocksuite/trunk/debian/README.Debian 2008-02-02 13:57:12 UTC (rev 1261)
@@ -5,7 +5,7 @@
simulation of the docking of fairly small chemical ligands to
rather big protein receptors. Earlier versions had all flexibility
in the ligands while the protein was kept rather ridgid. This latest
-version 4 also allows for a flexibility of the sidechains of surface
+version 4 also allows for a flexibility of selected sidechains of surface
residues, i.e., takes the rotamers into account.
This package was not yet tested in practice. Please give respective
@@ -14,23 +14,25 @@
package maintenance, just say "hello". The package compiles smoothly
on AMD64 and i686. More success stories are warmely welcomed.
-The upstream developers at Scripps have accompanies this package with
+The upstream developers at Scripps have accompanied this package with
a set of programs that are more prone to be used by the user directly.
-These are located in a separate package, the AutoDockTools. These are far more
-difficult to pack. A first attempt is available on Debian-Med underneath
-the packages/mgltools folder. More information is in the README at the
-same location.
+These are located in a separate package, the AutoDockTools and are
+far more difficult to pack for Debian. A first attempt is available on
+Debian-Med underneath the packages/mgltools folder. More information is
+in the README at the same location.
Garrett Morris of the upstream developers is very much looking forward to
-see AutoDock being distributed with Debian. Scripps requests registrations
-prior to the download of the tarball or the binaries at this URL:
+see AutoDock being distributed with Debian. The Scripps Institute asks for
+registrations prior to the download of the tarball or the binaries at this URL
- http://autodock.scripps.edu/downloads/autodock-registration.
+ http://autodock.scripps.edu/downloads/autodock-registration
-Please respect their interest to know about the impact their work has on the field,
-which is key for writing grant applications, and also install the Debian
-package popularity-contest. This counts the installations and may thus help
-upstream to further develop their software.
+which does not affect the distribution of this package under the
+GPL. Nevertheless, please respect upstream's genuine interest to know
+about the impact their work has on the field, which is key for writing
+grant applications. Also please consider installing the Debian package
+popularity-contest. This counts the installations and may thus further
+help upstream to further develop their software.
Steffen
Modified: trunk/packages/autodocksuite/trunk/debian/autodock4.1
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock4.1 2008-02-02 12:19:10 UTC (rev 1260)
+++ trunk/packages/autodocksuite/trunk/debian/autodock4.1 2008-02-02 13:57:12 UTC (rev 1261)
@@ -53,11 +53,27 @@
.B \-c |
.RI control_program
(Command mode, by control_program)
+.SH EXAMPLE
+
+On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute autodock as shown below:
+.br
+gunzip *.map.gz
+.br
+autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg
+
+The interpretation of results is aided by the AutoDockTools suite. Please also inspect the tutorials offered online.
+
.SH SEE ALSO
.BR autogrid (1),
.BR runAdt (1).
.br
http://autodock.scripps.edu
+.SH LICENSE
+This software is made available under the terms of the GNU Public
+License version 2 or later. This implies that this software may be
+redistributed if the source is made available. It would however help
+the future development of the AutoDockSuite if you register yourself
+at http://autodock.scripps.edu/downloads.
.SH AUTHOR
The most prominent author of the version 4 of autodock is G. Morris
<garrett at scripps.edu>. See the AUTHORS file in /usr/share/doc/autodock
Modified: trunk/packages/autodocksuite/trunk/debian/autogrid4.1
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autogrid4.1 2008-02-02 12:19:10 UTC (rev 1260)
+++ trunk/packages/autodocksuite/trunk/debian/autogrid4.1 2008-02-02 13:57:12 UTC (rev 1261)
@@ -1,7 +1,4 @@
.\" 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 AUTOGRID 1 "Juli 23, 2007"
.\" Please adjust this date whenever revising the manpage.
.\"
@@ -38,29 +35,55 @@
.\" TeX users may be more comfortable with the \fB<whatever>\fP and
.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
.\" respectively.
+.ad l
.SH OPTIONS
.TP
\fB\-o\fR
Use old PDBq format (q in columns 55-61)
-
.TP
+.B \-o
+Use old PDBq format (q in columns 55-61)
+.TP
+.B \-u
+Usage information, also \-h on Debian.
+.TP
.B \-d
Increased verbosity of messages to help debugging.
-
.TP
.B \-l
.RI logfile
-
.TP
.B \-p
.RI filename
Specifies Grid Parameter File
+.SH EXAMPLE
+A range of tests is made available with the AutoGrid sources that can be used as follows:
+.br
+$ D=/usr/share/doc/autogrid/Tests
+.br
+$ cd /tmp
+.br
+$ ln -s $D/AD4_parameters.dat .
+.br
+$ gunzip -c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
+.br
+.nh
+$ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l hsg1_no_receptor_types.glg
+.ad b
+.TP
+This command prepares grid files for each of the AutoDock atom types (hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. For performing the computation, autodock is executed, though it demands a separate parameter .dpf file that assignes these newly created files to the docking process and allows the setting of further parameters.
.SH SEE ALSO
.BR autodock (1),
.BR runAdt (1).
.br
http://autodock.scripps.edu
+.SH LICENSE
+This software is made available under the terms of the GNU Public
+License version 2 or later. This implies that this software may be
+redistributed if the source is made available. It would however help
+the future development of the AutoDockSuite if you register yourself
+at http://autodock.scripps.edu/downloads.
.SH AUTHOR
The most prominent author of the version 4 of autodock is G. Morris
<garrett at scripps.edu>. See the AUTHORS file in /usr/share/doc/autogrid
Modified: trunk/packages/autodocksuite/trunk/debian/control
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/control 2008-02-02 12:19:10 UTC (rev 1260)
+++ trunk/packages/autodocksuite/trunk/debian/control 2008-02-02 13:57:12 UTC (rev 1261)
@@ -14,22 +14,23 @@
Recommends: autogrid
Suggests: popularity-contest
Description: analysis of ligand binding to protein structure
- AutoDock is a well-established suite of programs for the molecular
- analysis the docking of a smaller chemical compounds to their receptors
- of known structure.
+ The AutoDockSuite addresses the molecular analysis of the docking of
+ a smaller chemical compounds to their receptors of known three-dimensional
+ structure.
.
- The AutoDock program performs the docking of the ligand to a set
- of grids describing the target protein. AutoGrid pre-calculates these grids.
+ The AutoDock program performs the docking of the ligand to a set of
+ grids describing the target protein. AutoGrid pre-calculates these grids.
Package: autogrid
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Suggests: autogrid, popularity-contest
Description: pre-calculate binding of ligands to their receptor
- AutoDock is a well-established suite of programs for the molecular
- analysis the docking of a smaller chemical compounds to their receptors
- of known structure.
+ The AutoDockSuite addresses the molecular analysis of the docking of
+ a smaller chemical compounds to their receptors of known three-dimensional
+ structure.
.
- The AutoGrid program performs pre-calculations for the docking of a ligand
- to a set of grids that describe the target protein. Detailed analyses are
- performed by the AutoDock program.
+ The AutoGrid program performs pre-calculations for the docking of a
+ ligand to a set of grids that describe the effect that the protein has
+ on point charges. The effect of these forces on the ligand are then
+ analysed by the AutoDock program.
Added: trunk/packages/autodocksuite/trunk/debian/patches/addHelp.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/addHelp.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/addHelp.patch 2008-02-02 13:57:12 UTC (rev 1261)
@@ -0,0 +1,12 @@
+Index: autodocksuite-4.0.1.obsolete.0.811087426104681/src/autogrid/setflags.cpp
+===================================================================
+--- autodocksuite-4.0.1.obsolete.0.811087426104681.orig/src/autogrid/setflags.cpp 2008-01-20 00:03:51.357536139 +0100
++++ autodocksuite-4.0.1.obsolete.0.811087426104681/src/autogrid/setflags.cpp 2008-01-20 00:04:42.874595186 +0100
+@@ -98,6 +98,7 @@
+ debug++;
+ break;
+ case 'u':
++ case 'h':
+ fprintf(stderr, "usage: %s %s\n", programname, AutoGridHelp);
+ exit(0);
+ break;
Added: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2008-02-02 13:57:12 UTC (rev 1261)
@@ -0,0 +1 @@
+addHelp.patch
Modified: trunk/packages/autodocksuite/trunk/debian/rules
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/rules 2008-02-02 12:19:10 UTC (rev 1260)
+++ trunk/packages/autodocksuite/trunk/debian/rules 2008-02-02 13:57:12 UTC (rev 1261)
@@ -16,8 +16,8 @@
# This has to be exported to make some magic below work.
export DH_OPTIONS
+include /usr/share/quilt/quilt.make
-
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
@@ -27,7 +27,7 @@
endif
configure: configure-stamp
-configure-stamp:
+configure-stamp: $(QUILT_STAMPFN)
dh_testdir
# Add here commands to configure the package.
for d in autodock autogrid; do \
@@ -52,7 +52,7 @@
#$(MAKE) doc
touch $@
-clean:
+clean: unpatch
dh_testdir
dh_testroot
rm -f build-arch-stamp build-indep-stamp configure-stamp
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