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

Scott Brozell sbrozell at rci.rutgers.edu
Fri Apr 6 00:46:23 PDT 2012


Hi,

Sticking with ########## appears to be the best approach.

Thanks everyone for the comments.
scott

ps.  
http://tripos.com/data/support/mol2.pdf
@<TRIPOS>COMMENT
Note: This RTI has not been implemented. Instead comments appear in the file
immediately above the @<TRIPOS>ATOM line.

On Wed, Apr 04, 2012 at 09:53:36PM +0200, Maciek Wójcikowski wrote:
> Maybe @<TRIPOS>COMMENT would be a better place for them?
> http://tripos.com/data/support/mol2.pdf
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> maciek at wojcikowski.pl
> 
> 
> W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang
> <conrad at 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 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<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/6846289/1afk_ligand_conformers.mol2>
> >>     > http://dl.dropbox.com/u/**6846289/3h78_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<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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