[Chimera-users] [Open Babel] UCSF Dock mol2 files
conrad at cgl.ucsf.edu
Wed Apr 4 11:08:54 PDT 2012
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.
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:
> 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
> > 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
> > 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
> > > > 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
> > > from
> > > > those files. Especially conformer ID is important for further
> > > > 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
> > >
> > > Cheers,
> > > -Geoff
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
More information about the Chimera-users