[Chimera-users] [Open Babel] UCSF Dock mol2 files
maciek at wojcikowski.pl
Wed Apr 4 12:53:36 PDT 2012
Maybe @<TRIPOS>COMMENT would be a better place for them?
Pozdrawiam, | Best regards,
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.
> 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
>> 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>>>
>> 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/6846289/1afk_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
>> > name and pass all 3 grid scores (total, vdw and ele) somehow (i
>> > 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>>>
>> > > > 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
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