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

[Maciek Wójcikowski]

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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>
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