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.<div>
<div><br></div><div>For Dock reference you can see dock6/src/dock/library_file.cpp it seams fairy simple and always uses ##########.<br><div>----<br>Pozdrawiam, | Best regards,<br>Maciek Wójcikowski<br><a href="mailto:maciek@wojcikowski.pl" target="_blank">maciek@wojcikowski.pl</a><br>
<br><br><div class="gmail_quote">W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <span dir="ltr"><<a href="mailto:sbrozell@rci.rutgers.edu">sbrozell@rci.rutgers.edu</a>></span> napisał:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
This is a good suggestion.<br>
<br>
But before implementation,<br>
1) do the DOCK developers or users have any comments ?<br>
2) do the Chimera developers or users have any comments ?<br>
In particular, does Chimera use ########## as the lexeme for the DOCK token ?<br>
It might be useful to have a consistent lexeme across programs.<br>
Or maybe the Babel folks have comments on what would be a more general tag ?<br>
<br>
thanks,<br>
scott<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:<br>
> Here you have two example files<br>
> <a href="http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2" target="_blank">http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2</a><br>
> <a href="http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2" target="_blank">http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2</a><br>
><br>
> What OB should do (in my mind) is to take "Name:" value as target molecule<br>
> name and pass all 3 grid scores (total, vdw and ele) somehow (i guess<br>
> comment is a right place, since there is not much choice), so that it can<br>
> output it in simmilar manner.<br>
><br>
> Maybe it would be easier to have an option "d" (aka. dock) which would copy<br>
> ALL the ###### data, and some other one, such as "s" (aka. sufix) to take<br>
> suffixed name into account. Disadvantage of above is that it wouldn't work<br>
> for other formats.<br>
> ----<br>
> Pozdrawiam, | Best regards,<br>
> Maciek Wójcikowski<br>
> <a href="mailto:maciek@wojcikowski.pl">maciek@wojcikowski.pl</a><br>
><br>
><br>
> W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <<br>
> <a href="mailto:geoff@geoffhutchison.net">geoff@geoffhutchison.net</a>> napisał:<br>
><br>
> > > I have a thought about mol2 files form Dock program, which contain<br>
> > > additional information in commentary (###). Those information is being<br>
> > lost<br>
> > > during openbabel operations, which is a pity. I'd like to propose a<br>
> > in/out<br>
> > > option for mol2 for Dock'ed mol2's to read/write compatible information<br>
> > from<br>
> > > those files. Especially conformer ID is important for further anylisis.<br>
> > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg<br>
> > files.<br>
> ><br>
> ><br>
> > If you can give us a selection of example files and a list of what<br>
> > information you'd like retained, it's fairly easy to patch the parsers.<br>
> ><br>
> > Cheers,<br>
> > -Geoff<br>
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