Hello,

I am trying to count how many times a given moiety can be found in a
database. My interest is not the list of the molecules containing this
substructure, but how many times it can be found. Let's say that in my
Database.smi file I have a biphenyl (c1ccc(cc1)c2ccccc2) and I want to
count how many times phenyl is found. If I try "obabel Database.smi -O
Output.smi -s "c1ccccc1"", it returns the biphenyl SMILES string in
Output.smi. However it is written only once whereas the phenyl moiety
appears twice in it.

Is there a way with obabel to return the value I am looking for (2 in
this case)? If the biphenyl is written twice, it is OK for me, at the
end I can do a "wc -l" on Output.smi.

If not, how can it be done with the API?

Thank you for your help.

Nicolas

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