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 solution is to filter out the big
molecules before doing substructure search, but openbabel does the substructure
search first, i.e.
obabel dbase.sdf -d --filter "atoms < 20" -O results.sdf -s trial.smi -al 9000
-ifs
gives the identical "too many candidates" message. Of course, I can keep
increasing "-al 9000" but that's a workaround and not the real solution.
For some reason, piping
obabel dbase.fs -d --filter "atoms < 20" -ocopy | obabel -ifs -O results.sdf -s
trial.smi -al 9000
stalls even at the first step --- it seems that one cannot filter "fs"
database, but I am not sure if I am using the correct syntax.
Best regards,
Vis
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