Hi all,
I am doing a similarity search between a query molecule given as a smiles
string and a database of molecules. This database has been properly indexed
with the command line. I am using MACCS fingerprints and programming in
Python. But actually I am seeing the same thing with the command line:
So I have noticed that, if my query is in the database, the output is
correct and the first compound of the list of similar compounds is my query
itself.
But when I give as -s option a smiles string that corresponds to a molecule
that is not present in the database, the first molecule of the output file
is not my query molecule anymore, but apparently one close molecule from my
database.
I have read here <http://openbabel.org/wiki/Tutorial:Fingerprints> this:
*note:* if the query molecule does not match the SMARTS string this will not
> work as expected, as the first molecule in the database that matches the
> SMARTS string will instead be used as the query
>
Is it what is happening to me? Is there a way to force the fingerprint
comparison between my *real query* and the database?
In case this is not possible, I was planning to use more programming, and
doing that I have a second question:
is it possible to get a Fingerprint object from a list of "on" bits? Using
SetBit() for example?
Thanks for any help,
Regards,
Floriane Montanari
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