[Dock-fans] Is there a way to separate the mol2 files in poses.mol2

Jonathan Gough jonathan.d.gough at gmail.com
Thu Jul 14 08:18:52 PDT 2016


Thanks,
Yes, I have looked at the file and am familiar with it's format. that being
said I wanted to check and see if something already existed before I went
ahead and re-invented the wheel. FWIW, vmd will only open a single pose.

Jonathan


On Thu, Jul 14, 2016 at 11:13 AM, lingling Jiang <jianglilian68 at gmail.com>
wrote:

> Hi Jonathan,
>
> Although the different poses are saved together in one multi-mol2
> file, the format of the file is rather simple. If you open it in vim,
> you should find that different poses are written in separate sections,
> each includes header and footer. It should be very straightforward to
> write a script to split the multi-mol2 file into separate mol2 files
> by simply searching for keywords in the header/footer.
>
> Also, you can try open and manipulate the multi-mol2 file using
> molecular modeling softwares such as VMD or Chimera. You might want to
> check their tutorials for further instructions.
>
> Hope this helps,
> Lingling
>
> On Thu, Jul 14, 2016 at 10:47 AM, Jonathan Gough
> <jonathan.d.gough at gmail.com> wrote:
> > Hi,
> >
> > After having done a docking expt and enrichment expt using the
> > combineScoresandPoses.py script you get a very large mol2 file that
> > wonderfully has all the poses together. I was wondering, Is there a way
> > within the other wonderful scripts you have put together to extract each
> of
> > the mol2 poses from the combined poses.mol2 file? Or can someone point
> me in
> > the right direction towards some code in the scripts to look at in terms
> of
> > trying to figure out how to write something like that for myself?
> >
> > thanks,
> > Jonathan
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://mailman.docking.org/mailman/listinfo/dock-fans
> >
>
>
>
> --
> Best,
> Lingling Jiang
> Postdoctoral Research Scientist, Tavazoie Lab
> Dept. of Systems Biology, Columbia University
>
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