Maybe @<TRIPOS>COMMENT would be a better place for them?<div><a href="http://tripos.com/data/support/mol2.pdf">http://tripos.com/data/support/mol2.pdf</a> <br clear="all">----<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 4 kwietnia 2012 20:08 użytkownik Conrad Huang <span dir="ltr"><<a href="mailto:conrad@cgl.ucsf.edu">conrad@cgl.ucsf.edu</a>></span> napisał:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
<br>
Conrad<div class="im"><br>
<br>
On 4/3/12 2:22 PM, Maciek Wójcikowski wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
For Chimera reference check out file<br>
UCSF-Chimera-XXX/share/<u></u>ViewDock/Compound.py You can see many versions of<br>
Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the<br>
same comment method. This comments are only used by ViewDock module, as<br>
far as I know.<br>
<br>
For Dock reference you can see dock6/src/dock/library_file.<u></u>cpp it seams<br>
fairy simple and always uses ##########.<br>
----<br>
Pozdrawiam, | Best regards,<br>
Maciek Wójcikowski<br>
</div><a href="mailto:maciek@wojcikowski.pl" target="_blank">maciek@wojcikowski.pl</a> <mailto:<a href="mailto:maciek@wojcikowski.pl" target="_blank">maciek@wojcikowski.pl</a>><div class="im"><br>
<br>
<br>
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell<br></div>
<<a href="mailto:sbrozell@rci.rutgers.edu" target="_blank">sbrozell@rci.rutgers.edu</a> <mailto:<a href="mailto:sbrozell@rci.rutgers.edu" target="_blank">sbrozell@rci.rutgers.<u></u>edu</a>>> napisał:<div><div class="h5">
<br>
<br>
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<br>
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<br>
general tag ?<br>
<br>
thanks,<br>
scott<br>
<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/<u></u>6846289/1afk_ligand_<u></u>conformers.mol2</a><br>
> <a href="http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2" target="_blank">http://dl.dropbox.com/u/<u></u>6846289/3h78_ligand_<u></u>conformers.mol2</a><br>
><br>
> What OB should do (in my mind) is to take "Name:" value as target<br>
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<br>
that it can<br>
> output it in simmilar manner.<br>
><br>
> Maybe it would be easier to have an option "d" (aka. dock) which<br>
would copy<br>
> ALL the ###### data, and some other one, such as "s" (aka. sufix)<br>
to take<br>
> suffixed name into account. Disadvantage of above is that it<br>
wouldn't work<br>
> for other formats.<br>
> ----<br>
> Pozdrawiam, | Best regards,<br>
> Maciek Wójcikowski<br></div></div>
> <a href="mailto:maciek@wojcikowski.pl" target="_blank">maciek@wojcikowski.pl</a> <mailto:<a href="mailto:maciek@wojcikowski.pl" target="_blank">maciek@wojcikowski.pl</a>><div class="im"><br>
><br>
><br>
> W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <<br></div>
> <a href="mailto:geoff@geoffhutchison.net" target="_blank">geoff@geoffhutchison.net</a> <mailto:<a href="mailto:geoff@geoffhutchison.net" target="_blank">geoff@geoffhutchison.<u></u>net</a>>> napisał:<div class="im">
<br>
><br>
> > > I have a thought about mol2 files form Dock program, which<br>
contain<br>
> > > additional information in commentary (###). Those information<br>
is being<br>
> > lost<br>
> > > during openbabel operations, which is a pity. I'd like to<br>
propose a<br>
> > in/out<br>
> > > option for mol2 for Dock'ed mol2's to read/write compatible<br>
information<br>
> > from<br>
> > > those files. Especially conformer ID is important for further<br>
anylisis.<br>
> > > Simmilar approach is used with pdbqt's contained in<br>
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<br>
parsers.<br>
> ><br>
> > Cheers,<br>
> > -Geoff<br>
<br>
<br>
<br>
<br></div>
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</blockquote>
</blockquote></div><br></div>