Hi,
15 aug 2012 kl. 10:22 skrev Kareem Khoury:
> Two questions, one of which Im sure is very simple question but i cant seem
> to figure it out
>
> 1)
> When i type in the command for obfit:
>
> obfit smartscode ref.sdf library.sdf
>
> it give me the output only in the command prompt window.
>
> I tried adding -o and ouputfile.sd and nothing happened. How do i get the
> program to give me the output to an sd or sdf file?
>
To do this, you redirect the output to a file like
obfit smartscode ref.sdf library.sdf > outfile.sdf
> 2)
> Is it possible with this program to fit patterns that are not compleatly
> similar ie if i have a library of compounds with pyrimidines and pyridines
> could i fit that to a benzyle ring?
Yes, with the correct SMARTS string it's possible. In your case you should use
"[c,n]1c[c,n]ccc1".
Kind regards,
Fredrik
>
> Thanks
>
> -Kareem
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