Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:
Here you have two example files http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2
What OB should do (in my mind) is to take "Name:" value as target molecule name and pass all 3 grid scores (total, vdw and ele) somehow (i guess comment is a right place, since there is not much choice), so that it can output it in simmilar manner.
Maybe it would be easier to have an option "d" (aka. dock) which would copy ALL the ###### data, and some other one, such as "s" (aka. sufix) to take suffixed name into account. Disadvantage of above is that it wouldn't work for other formats. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl
W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < geoff@geoffhutchison.net> napisał:
I have a thought about mol2 files form Dock program, which contain additional information in commentary (###). Those information is being lost during openbabel operations, which is a pity. I'd like to propose a in/out option for mol2 for Dock'ed mol2's to read/write compatible information from those files. Especially conformer ID is important for further anylisis. Simmilar approach is used with pdbqt's contained in Autodock's .dlg files.
If you can give us a selection of example files and a list of what information you'd like retained, it's fairly easy to patch the parsers.
Cheers, -Geoff