http://tripos.com/data/support/mol2.pdf
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
maciek@wojcikowski.pl

W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang <conrad@cgl.ucsf.edu> napisał:

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@wojcikowski.pl <mailto:maciek@wojcikowski.pl>

W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell
<sbrozell@rci.rutgers.edu <mailto:sbrozell@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@wojcikowski.pl <mailto:maciek@wojcikowski.pl>

>
>
> W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <
> geoff@geoffhutchison.net <mailto: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

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