[med-svn] r5422 - trunk/packages/autodock-vina/trunk/debian
yask gupta
yask-guest at alioth.debian.org
Thu Nov 11 15:48:42 UTC 2010
Author: yask-guest
Date: 2010-11-11 15:48:37 +0000 (Thu, 11 Nov 2010)
New Revision: 5422
Added:
trunk/packages/autodock-vina/trunk/debian/manpages
trunk/packages/autodock-vina/trunk/debian/vina.1
trunk/packages/autodock-vina/trunk/debian/vina_split.1
Removed:
trunk/packages/autodock-vina/trunk/debian/manpage.1.ex
trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex
Modified:
trunk/packages/autodock-vina/trunk/debian/README.source
Log:
Added man pages.
Modified: trunk/packages/autodock-vina/trunk/debian/README.source
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/README.source 2010-11-11 15:40:24 UTC (rev 5421)
+++ trunk/packages/autodock-vina/trunk/debian/README.source 2010-11-11 15:48:37 UTC (rev 5422)
@@ -9,3 +9,7 @@
http://vina.scripps.edu/manual.html#build
and an otherwise missing Makefile added to
allow the direct application of cdbs.
+
+The man pages were created with help2man
+(also available as a Debian package) and
+are overdue to be manually improved.
Deleted: trunk/packages/autodock-vina/trunk/debian/manpage.1.ex
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpage.1.ex 2010-11-11 15:40:24 UTC (rev 5421)
+++ trunk/packages/autodock-vina/trunk/debian/manpage.1.ex 2010-11-11 15:48:37 UTC (rev 5422)
@@ -1,59 +0,0 @@
-.\" 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 AUTODOCK-VINA SECTION "November 11, 2010"
-.\" 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
-autodock-vina \- program to do something
-.SH SYNOPSIS
-.B autodock-vina
-.RI [ options ] " files" ...
-.br
-.B bar
-.RI [ options ] " files" ...
-.SH DESCRIPTION
-This manual page documents briefly the
-.B autodock-vina
-and
-.B bar
-commands.
-.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.
-\fBautodock-vina\fP is a program that...
-.SH OPTIONS
-These programs follow the usual GNU command line syntax, with long
-options starting with two dashes (`-').
-A summary of options is included below.
-For a complete description, see the Info files.
-.TP
-.B \-h, \-\-help
-Show summary of options.
-.TP
-.B \-v, \-\-version
-Show version of program.
-.SH SEE ALSO
-.BR bar (1),
-.BR baz (1).
-.br
-The programs are documented fully by
-.IR "The Rise and Fall of a Fooish Bar" ,
-available via the Info system.
-.SH AUTHOR
-autodock-vina was written by <upstream author>.
-.PP
-This manual page was written by yask <yask.gupta87 at gmail.com>,
-for the Debian project (and may be used by others).
Deleted: trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex 2010-11-11 15:40:24 UTC (rev 5421)
+++ trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex 2010-11-11 15:48:37 UTC (rev 5422)
@@ -1,154 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
- <!ENTITY dhsurname "<surname>SURNAME</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>November 11, 2010</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
- <!ENTITY dhemail "<email>yask.gupta87 at gmail.com</email>">
- <!ENTITY dhusername "yask">
- <!ENTITY dhucpackage "<refentrytitle>AUTODOCK-VINA</refentrytitle>">
- <!ENTITY dhpackage "autodock-vina">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>program to do something</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
-
- <arg><option>-e <replaceable>this</replaceable></option></arg>
-
- <arg><option>--example <replaceable>that</replaceable></option></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> and <command>bar</command>
- commands.</para>
-
- <para>This manual page was written for the &debian; distribution
- because the original program does not have a manual page.
- Instead, it has documentation in the &gnu;
- <application>Info</application> format; see below.</para>
-
- <para><command>&dhpackage;</command> is a program that...</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
-
- <para>These programs follow the usual &gnu; command line syntax,
- with long options starting with two dashes (`-'). A summary of
- options is included below. For a complete description, see the
- <application>Info</application> files.</para>
-
- <variablelist>
- <varlistentry>
- <term><option>-h</option>
- <option>--help</option>
- </term>
- <listitem>
- <para>Show summary of options.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-v</option>
- <option>--version</option>
- </term>
- <listitem>
- <para>Show version of program.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
-
- <para>bar (1), baz (1).</para>
-
- <para>The programs are documented fully by <citetitle>The Rise and
- Fall of a Fooish Bar</citetitle> available via the
- <application>Info</application> system.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (and 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.
- </para>
- <para>
- On Debian systems, the complete text of the GNU General Public
- License can be found in /usr/share/common-licenses/GPL.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
-sgml-indent-step:2
-sgml-indent-data:t
-sgml-parent-document:nil
-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
Added: trunk/packages/autodock-vina/trunk/debian/manpages
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpages (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/manpages 2010-11-11 15:48:37 UTC (rev 5422)
@@ -0,0 +1,2 @@
+debian/vina.1
+debian/vina_split.1
Added: trunk/packages/autodock-vina/trunk/debian/vina.1
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/vina.1 (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/vina.1 2010-11-11 15:48:37 UTC (rev 5422)
@@ -0,0 +1,86 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1.
+.TH AUTODOCK "1" "November 2010" "AutoDock Vina 1.1.1 (Apr 20, 2010)" "User Commands"
+.SH NAME
+AutoDock \- manual page for AutoDock Vina 1.1.1 (Apr 20, 2010)
+.SH DESCRIPTION
+.SS "Input:"
+.TP
+\fB\-\-receptor\fR arg
+rigid part of the receptor (PDBQT)
+.TP
+\fB\-\-flex\fR arg
+flexible side chains, if any (PDBQT)
+.TP
+\fB\-\-ligand\fR arg
+ligand (PDBQT)
+.SS "Search space (required):"
+.TP
+\fB\-\-center_x\fR arg
+X coordinate of the center
+.TP
+\fB\-\-center_y\fR arg
+Y coordinate of the center
+.TP
+\fB\-\-center_z\fR arg
+Z coordinate of the center
+.TP
+\fB\-\-size_x\fR arg
+size in the X dimension (Angstroms)
+.TP
+\fB\-\-size_y\fR arg
+size in the Y dimension (Angstroms)
+.TP
+\fB\-\-size_z\fR arg
+size in the Z dimension (Angstroms)
+.SS "Output (optional):"
+.TP
+\fB\-\-out\fR arg
+output models (PDBQT), the default is chosen based on
+the ligand file name
+.TP
+\fB\-\-log\fR arg
+optionally, write log file
+.SS "Misc (optional):"
+.TP
+\fB\-\-cpu\fR arg
+the number of CPUs to use (the default is to try to
+detect the number of CPUs or, failing that, use 1)
+.TP
+\fB\-\-seed\fR arg
+explicit random seed
+.TP
+\fB\-\-exhaustiveness\fR arg (=8) exhaustiveness of the global search (roughly
+proportional to time): 1+
+.TP
+\fB\-\-num_modes\fR arg (=9)
+maximum number of binding modes to generate
+.TP
+\fB\-\-energy_range\fR arg (=3)
+maximum energy difference between the best binding
+mode and the worst one displayed (kcal/mol)
+.SS "Configuration file (optional):"
+.TP
+\fB\-\-config\fR arg
+the above options can be put here
+.SS "Information (optional):"
+.TP
+\fB\-\-help\fR
+display usage summary
+.TP
+\fB\-\-help_advanced\fR
+display usage summary with advanced options
+.TP
+\fB\-\-version\fR
+display program version
+.SH "SEE ALSO"
+The full documentation for
+.B AutoDock
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B AutoDock
+programs are properly installed at your site, the command
+.IP
+.B info AutoDock
+.PP
+should give you access to the complete manual.
Added: trunk/packages/autodock-vina/trunk/debian/vina_split.1
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/vina_split.1 (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/vina_split.1 2010-11-11 15:48:37 UTC (rev 5422)
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1.
+.TH AUTODOCK "1" "November 2010" "AutoDock Vina PDBQT Split 1.1.1 (Apr 20, 2010)" "User Commands"
+.SH NAME
+AutoDock \- manual page for AutoDock Vina PDBQT Split 1.1.1 (Apr 20, 2010)
+.SH DESCRIPTION
+.SS "Input:"
+.TP
+\fB\-\-input\fR arg
+input to split (PDBQT)
+.SS "Output (optional) - defaults are chosen based on the input file name:"
+.TP
+\fB\-\-ligand\fR arg
+prefix for ligands
+.TP
+\fB\-\-flex\fR arg
+prefix for side chains
+.SS "Information (optional):"
+.TP
+\fB\-\-help\fR
+print this message
+.TP
+\fB\-\-version\fR
+print program version
+.SH "SEE ALSO"
+The full documentation for
+.B AutoDock
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B AutoDock
+programs are properly installed at your site, the command
+.IP
+.B info AutoDock
+.PP
+should give you access to the complete manual.
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