[med-svn] r7350 - trunk/packages/mgltools/autodocktools/trunk/debian

[Steffen Möller]

Author: moeller
Date: 2011-07-30 08:48:10 +0000 (Sat, 30 Jul 2011)
New Revision: 7350

Added:
   trunk/packages/mgltools/autodocktools/trunk/debian/autoligand.1
Modified:
   trunk/packages/mgltools/autodocktools/trunk/debian/README.Debian
   trunk/packages/mgltools/autodocktools/trunk/debian/autodocktools.links
   trunk/packages/mgltools/autodocktools/trunk/debian/manpages
Log:
More towards autoligand.


Modified: trunk/packages/mgltools/autodocktools/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/README.Debian	2011-07-30 00:30:20 UTC (rev 7349)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/README.Debian	2011-07-30 08:48:10 UTC (rev 7350)
@@ -20,8 +20,8 @@
 longer for a DFSG compatible license, though.
 
 If you are a regular user of this package, your feedback to us
-packagers would much appreciated. The packaging is organised
+packagers would be much appreciated. The packaging is organised
 via the Debian-Med alioth project that has its own portal on
-http://debian-med.alioth.debian.org.
+http://debian-med.alioth.debian.org and a mailing list that listens.
 
  -- Steffen Moeller <moeller at debian.org>  Sun, 20 Jul 2008 00:33:11 +0200

Modified: trunk/packages/mgltools/autodocktools/trunk/debian/autodocktools.links
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/autodocktools.links	2011-07-30 00:30:20 UTC (rev 7349)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/autodocktools.links	2011-07-30 08:48:10 UTC (rev 7350)
@@ -1,2 +1,3 @@
 /usr/bin/runAdt /usr/bin/autodocktools
 /usr/share/man/man1/runAdt.1.gz /usr/share/man/man1/autodocktools.1.gz
+/usr/share/pyshared/AutoDockTools/AutoLigand.py /usr/bin/autoligand

Added: trunk/packages/mgltools/autodocktools/trunk/debian/autoligand.1
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/autoligand.1	                        (rev 0)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/autoligand.1	2011-07-30 08:48:10 UTC (rev 7350)
@@ -0,0 +1,54 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
+.TH AUTOLIGAND "1" "July 2011" "AutoLigand" "User Commands"
+.SH NAME
+AutoLigand: \- identification of a receptor's ligand binding site
+.SH SYNOPSIS
+It is suggested to start AutoLigand through the GUI that the 
+autodocktools provide.
+.BR
+.B autoligand
+\f-r FileBaseName -p #_of_pts\fR
+.BR
+The above is a simplification provided for the Debian package. The regular
+command line invocation is through
+.BR
+python /usr/share/pyshared/AutoDockTools/AutoLigand.py \fB\-r\fR FileBaseName \fB\-p\fR #_of_pts
+.SH DESCRIPTION
+.I autoligand
+is a symbolic link to the Python script AutoLigand.py. That performs
+a an automated investigation of the likelihood of a particular 
+part of a protein to bind to ligands.
+.IP
+Description of command...
+.HP
+\fB\-r\fR FileBaseName = just the name part from receptor map files (i.e., FileBaseName.C.map)
+.HP
+\fB\-p\fR #_of_pts = number of fill points to use (int)
+.IP
+Note: can be omitted if \fB\-a\fR option used.
+.IP
+Optional parameters:
+.IP
+[\-a #] = number of heavy atom for ligand (#_of_pts will be set to 6x atoms)
+.BR
+[\-x # \fB\-y\fR # \fB\-z\fR #] = optional x,y,z co\-ords for starting fill (float)
+.IP
+when starting point is input, only one fill will be run
+.IP
+[\-i # \fB\-j\fR # \fB\-k\fR #] = optional x,y,z co\-ords for second point (float)
+.IP
+when second point is input, the fill will connect both points
+NOTE: the connection path has not been optimized \- use with discretion
+.IP
+[\-f #] = number of fills to generate \- default is 10
+.BR
+[\-e] = use the extra atom types NA, N, SA, and A
+.IP
+NOTE: these results can be problematic \- use with discretion
+.IP
+[\-m] = make a movie of output fill progress
+.SH "SEE ALSO"
+A tutorial is available online on
+http://autodock.scripps.edu/resources/autoligand/AutoLigand_tutorial.pdf
+.SH AUTHORS
+Rodney M. Harris and colleagues at The Scripps Institute, San Diego, California

Modified: trunk/packages/mgltools/autodocktools/trunk/debian/manpages
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/manpages	2011-07-30 00:30:20 UTC (rev 7349)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/manpages	2011-07-30 08:48:10 UTC (rev 7350)
@@ -1 +1,2 @@
 debian/runAdt.1
+debian/autoligand.1