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 <[email protected]>, -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>[email protected]</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. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
