[Chimera-users] [Open Babel] UCSF Dock mol2 files
sbrozell at rci.rutgers.edu
Tue Apr 3 12:13:01 PDT 2012
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 ?
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:
> Here you have two example files
> 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 at wojcikowski.pl
> W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <
> geoff at 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
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