[Chimera-users] [Open Babel] UCSF Dock mol2 files

[Maciek Wójcikowski]

For Chimera reference check out file
UCSF-Chimera-XXX/share/ViewDock/Compound.py You can see many versions of
Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the
same comment method. This comments are only used by ViewDock module, as far
as I know.

For Dock reference you can see dock6/src/dock/library_file.cpp it seams
fairy simple and always uses ##########.
----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
maciek at wojcikowski.pl


W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <
sbrozell at rci.rutgers.edu> napisał:

> 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 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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