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

William Joseph Allen william.joseph.allen at gmail.com
Thu Jul 14 08:21:08 PDT 2016

Hi Jonathan,

Here is an example of a script as Lingling mentioned. This one was written
by probably either Sudipto Mukherjee or Trent Balius. It assumes that the
first header line of each molecule in the multi-mol2 file starts with
"########## Name: ". It also will name the individual output mol2 files as
"<name>.mol2", where the name is whatever is on that first Name line. Be
cautious, though, because redundant names will overwrite files. This worked
well for us because we did a lot with ZINC molecules, which all had unique
names on that line.

In principal you should be able to easily modify this script if your
molecules have different header fields, or if you want to implement a
counter for example and just name each molecule by the index.

(Sometimes dock-fans is weird and doesn't allow attachments, so let me know
if you can't see the attached python script).


On Thu, Jul 14, 2016 at 10:18 AM, Jonathan Gough <jonathan.d.gough at gmail.com
> wrote:

> 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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