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