[Dock-fans] how to convert mol2 format to sdf format?
sbrozell at scripps.edu
Fri Jul 11 15:34:38 PDT 2008
On Fri, 11 Jul 2008, Andrew Harris Wiser wrote:
> One of the issues I ran into when converting Dock results
> from mol2 to sdf was extracting the scores from the
> comment fields for each compound. I tried performing
> conversions in both openbabel and Pipeline Pilot, but in
> both cases the comment fields were lost making analysis of
> the results outside of ViewDock tedious. I ended up
> writing a short perl script to extract the comment fields
> into a tab delimited file that can be easily merged in
> Pipeline Pilot. While this is an extra step in converting
> formats, the end result, an sdf file where each compound
> has properties reflecting the results from Dock, is very
> This is something I thought you might want to consider in
> addition to the actual conversion process since some of
> the data gets lost in translation. I tested the website
> provided and it too seemed to have this problem.
> As a side note is there a way to output the scores from
> Dock into fields that do not require this extra step? I'm
> still learning Dock, but I didn't see an option to change
> this. Based on the mol2 format specifications it seemed
> like mol2 files do not have the freedom of sdf/sd/mol
> files with property fields.
No way, except via source code modifications.
If you have a specific proposal with an example then we
shall consider it.
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