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

[Conrad Huang]

Our approach to file formats in Chimera is to support the "native" form 
from the developers.  The use of ########## for Dock mol2 format is 
obviously easiest for us since it is in use and already works in 
Chimera, but we're happy to accommodate a more broadly useful format.

Conrad

On 4/3/12 2:22 PM, Maciek Wójcikowski wrote:
> 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 <mailto:maciek at wojcikowski.pl>
>
>
> W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell
> <sbrozell at rci.rutgers.edu <mailto: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 <mailto:maciek at wojcikowski.pl>
>      >
>      >
>      > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <
>      > geoff at geoffhutchison.net <mailto: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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