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@wojcikowski.pl
W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang <conrad@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@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <sbrozell@rci.rutgers.edu <mailto:sbrozell@rci.rutgers.**edu<sbrozell@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@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
> > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff@geoffhutchison.net <mailto:geoff@geoffhutchison.**net<geoff@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