Dear all,
I am trying to look for certain molecules in the sdf/fs database containing
certain fragments as substructure. The problem is my fragments can be small (I
am running a script to do multiple searches), so I can get "too many candidates
in the fingerprint search phase". The simple solut
Express your substructure as SMARTS and use:
obabel dbase.sdf -s "SMARTS" -O results.sdf
If you are doing multiple searches (i.e. different SMARTS each time)
you can do it in one go (I think) as SMARTS has an OR syntax.
- Noel
On 20 November 2012 08:03, Visvaldas K. wrote:
> Dear all,
>
> I
On 20/11/2012 08:03, Visvaldas K. wrote:
> Dear all,
>
> I am trying to look for certain molecules in the sdf/fs database
> containing certain fragments as substructure. The problem is my
> fragments can be small (I am running a script to do multiple searches),
> so I can get "too many candidates i
Thank you Chris and Noel, but I am afraid I cannot use your advice, because
what I am trying to do is to search "each molecule in the DB as a substructure
against all molecules in the same DB", one by one, applying all possible
permutations using a script; for this reason I can't decide beforeha
Dear all,
I can't find any information about the MMFF94s force field (as opposed to
just MMFF94). Is this available in open babel? Also, is there a way to list
available forcefields interactively within python?
Best wishes,
Scott
--
View this message in context:
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>>> import pybel
>>> pybel.forcefields
['gaff', 'ghemical', 'mmff94', 'mmff94s', 'uff']
On 20 November 2012 12:37, scott_m wrote:
> Dear all,
>
> I can't find any information about the MMFF94s force field (as opposed to
> just MMFF94). Is this available in open babel? Also, is there a way to list
