[med-svn] r1063 - in trunk/packages/mgltools: autodocktools/trunk/debian mslib/trunk/debian pmv/trunk/debian

smoe-guest at alioth.debian.org smoe-guest at alioth.debian.org
Thu Jan 3 01:09:50 UTC 2008 

Author: smoe-guest
Date: 2008-01-03 01:09:50 +0000 (Thu, 03 Jan 2008)
New Revision: 1063

Added:
   trunk/packages/mgltools/autodocktools/trunk/debian/runAdt.1
   trunk/packages/mgltools/mslib/trunk/debian/README.Debian
   trunk/packages/mgltools/pmv/trunk/debian/runPmv.1
Log:
* man pages added for Pmv and Adt
* mslib now offers README.Debian


Added: trunk/packages/mgltools/autodocktools/trunk/debian/runAdt.1
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/runAdt.1	                        (rev 0)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/runAdt.1	2008-01-03 01:09:50 UTC (rev 1063)
@@ -0,0 +1,113 @@
+.\"                                      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 ADT 1 "Januar  2, 2008"
+.\" 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
+adt \- prepare proteins and ligands to analyse their binding
+.SH SYNOPSIS
+.B runAdt
+.RI [ options ]
+
+.SH DESCRIPTION
+This manual page is an almost literal translation of the output
+provided by 
+.B runAdt -h
+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.
+For a complete description, refer to the tutorials and documentation
+that is available online.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-a or \-\-again
+play back lastlog file
+.TP
+.B \-\-overwriteLog
+overwrite log file
+.TP
+.B \-\-uniqueLog
+create a log file with a unique name
+.TP
+.B \-\-noLog
+turn off logging
+.TP
+.B \-\-noSplash
+turn off Splash Screen
+.TP
+.B \-\-die
+do not start GUI event loop
+.TP
+.B \-\-customizer file
+run the user specified file
+.TP
+.B \-\-lib packageName
+add a libraries of commands
+.TP
+.B \-v r, \-\-vision run
+run vision networks on the command line
+.TP
+.B \-v o, \-\-vision once
+run vision networks and exit ADT
+
+.TP
+.B \-d or \-\-dmode modes
+specify a display mode
+                modes can be any a combination of display mode
+               'cpk'  : cpk
+               'lines': lines
+               'ss'   : secondary structure ribbon
+               'sb'   : sticks and balls
+               'lic'  : licorice
+               'ms'   : molecular surface
+               'ca'   : C-alpha trace
+               'bt'   : backbone trace
+               'sp'   : CA-spline
+               'sssb' : secondary structure for proteins, sticks and balls for other residues with bonds lines for other residues without bonds
+
+.TP
+.B \-c or \-\-cmode modes
+specify a dispaly mode color scheme:
+                'ca' : color by atom
+                'cr' : color by residue (RASMOL scheme)
+                'cc' : color by chain
+                'cm' : color by molecule
+                'cdg': color using David Goodsell's scheme
+                'cs' : color residues using Shapely scheme
+                'css': color by secondary structure element
+
+.SH EXAMPLE:
+display protein as ribbon, non protein as sticks and balls
+and color by atom type
+.TP
+pmv -i --dmode sssb --cmode cr myprot.pdb
+.TP
+pmv -i -m sssb -c cr myprot.pdb
+
+
+.SH SEE ALSO
+.BR http://mgltools.scripps.edu
+.SH AUTHOR
+AutoDockTools was written by researchers of the Molecular
+Graphics Lab at the Scripps Institute <mgltools at scripps.edu>.
+.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/mgltools/mslib/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mgltools/mslib/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/mgltools/mslib/trunk/debian/README.Debian	2008-01-03 01:09:50 UTC (rev 1063)
@@ -0,0 +1,11 @@
+Debian package for the MS library
+=================================
+
+The sources come with precompiled libraries for the Molecular Surfaces library
+http://mgl.scripps.edu/people/sanner/html/msms_home.html
+
+This is rather unfortunate and may block the inclusion with the Debian main distribution.
+
+Steffen
+
+Thu, 03 Jan 2008 01:15:11 +0100

Added: trunk/packages/mgltools/pmv/trunk/debian/runPmv.1
===================================================================
--- trunk/packages/mgltools/pmv/trunk/debian/runPmv.1	                        (rev 0)
+++ trunk/packages/mgltools/pmv/trunk/debian/runPmv.1	2008-01-03 01:09:50 UTC (rev 1063)
@@ -0,0 +1,122 @@
+.\"                                      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 PMV 1 "Januar  2, 2008"
+.\" 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
+adt \- prepare proteins and ligands to analyse their binding
+.SH SYNOPSIS
+.B runPmv
+.RI [ options ]
+
+.SH DESCRIPTION
+This manual page is an almost literal translation of the output
+provided by 
+.B runPmv -h
+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.
+For a complete description, refer to the tutorials and documentation
+that is available online.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-a or \-\-again
+play back lastlog file
+.TP
+.B \-\-overwriteLog
+overwrite log file
+.TP
+.B \-\-uniqueLog
+create a log file with a unique name
+.TP
+.B \-\-noLog
+turn off logging
+.TP
+.B \-\-noSplash
+turn off Splash Screen
+.TP
+.B \-\-die
+do not start GUI event loop
+.TP
+.B \-\-customizer file
+run the user specified file
+.TP
+.B \-\-lib packageName
+add a libraries of commands
+.TP
+.B \-v r, \-\-vision run
+run vision networks on the command line
+.TP
+.B \-v o, \-\-vision once
+run vision networks and exit ADT
+
+.TP
+.B \-d or \-\-dmode modes
+specify a display mode
+
+modes can be any a combination of display mode
+ 'cpk'  : cpk
+ 'lines': lines
+ 'ss'   : secondary structure ribbon
+ 'sb'   : sticks and balls
+ 'lic'  : licorice
+ 'ms'   : molecular surface
+ 'ca'   : C-alpha trace
+ 'bt'   : backbone trace
+ 'sp'   : CA-spline
+ 'sssb' : secondary structure for proteins, sticks and balls for other residues with bonds lines for other residues without bonds
+
+.TP
+.B \-c or \-\-cmode modes
+specify a dispaly mode color scheme:
+ 'ca' : color by atom
+ 'cr' : color by residue (RASMOL scheme)
+ 'cc' : color by chain
+ 'cm' : color by molecule
+ 'cdg': color using David Goodsell's scheme
+ 'cs' : color residues using Shapely scheme
+ 'css': color by secondary structure element
+
+.TP
+.B \-\-update [nightly|tested|clear]
+Updates MGLTools. If no arguments are given then the Update Manager GUI is provided
+ 'nightly': download and install Nightly Builds
+ 'tested' : download and install tested Nightly Builds
+ 'clear'  : clear/uninstall all the updates
+
+
+.SH EXAMPLE:
+display protein as ribbon, non protein as sticks and balls
+and color by atom type
+.TP
+pmv -i --dmode sssb --cmode cr myprot.pdb
+.TP
+pmv -i -m sssb -c cr myprot.pdb
+
+
+.SH SEE ALSO
+.BR http://mgltools.scripps.edu
+.SH AUTHOR
+AutoDockTools was written by researchers of the Molecular
+Graphics Lab at the Scripps Institute <mgltools at scripps.edu>.
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (but may be used by others).

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