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 > mac...@wojcikowski.pl > > > W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang > <con...@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 > >> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> > >> > >> > >> > >> W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell > >> <sbroz...@rci.rutgers.edu > >> <mailto:sbrozell@rci.rutgers.**edu<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/6846289/1afk_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 > >> > mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> > >> > >> > > >> > > >> > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > >> > ge...@geoffhutchison.net > >> <mailto:geoff@geoffhutchison.**net<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 ------------------------------------------------------------------------------ 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
