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 > mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> > > > W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell > <sbroz...@rci.rutgers.edu <mailto:sbroz...@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 > > mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> > > > > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > > ge...@geoffhutchison.net <mailto:ge...@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 > > > > > _______________________________________________ > Chimera-users mailing list > chimera-us...@cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
