Maybe @TRIPOSCOMMENT 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.edunapisał:
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.**edusbroz...@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.mol2http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2
http://dl.dropbox.com/u/**6846289/3h78_ligand_**conformers.mol2http://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.**netge...@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-usershttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
