[Dock-fans] how to convert mol2 format to sdf format?

Scott Brozell sbrozell at scripps.edu
Fri Jul 11 15:34:38 PDT 2008


Hi,

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 
> useful.
> 
> 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.

Scott




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