Hi, no, I'm not planning to develop a solution without the dependency of autodocktools. The plugin is just a tool to use autodock and vina from within a pymol session. The Autodocktools are used for receptor and ligand preparation which is an essential part of a docking protocol, equally important to scoring functions and the docking algorithm itself. If a ligand is not correctly prepared (e.g., incorrect assignment of rotatable bonds, protonation state) you will never end ab with the correct result. Hence, this is a quite sophisticated functionality that cannot be replaced with a few lines of additional code and I'm therefore not putting any effort in this direction.
Cheers, Daniel On Friday 07 May 2010 06:14:14 pm Michael Banck wrote: > Hi, > > On Tue, Feb 16, 2010 at 08:26:00PM +0100, Daniel Seeliger wrote: > > take a look into > > ~/.ADplugin/pymol_autodock_plugin.conf > > and set the path to the autodocktools scripts correctly. Then the plugin > > should find them. > > Speaking of which, I was just taking a look about including your autodock > plugin (it looks really nice) into the official Debian/Ubuntu packages, > however, it depends on the non-free autodocktools scripts as far as I > can tell. > > While autodocktools is shipped in Debian non-free, we will not be able > to fully integrate this easily in order to keep pymol in Debian proper. > > Is there any work-around to get a fully free autodock plugin solution > and/or is it planned to reimplement the missing parts from autodocktools > in the autodock pymol plugin or maybe pymol itself? > > > Thanks, > > Michael > > --------------------------------------------------------------------------- > --- > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
