Hi George,
On Fri, Nov 8, 2013 at 5:02 PM, George Papadatos <[email protected]>wrote:
> Hi there,
> DB-related question again:
> When I retrieve fps from a postgres db, they look like this:
>
> \x020c00102204000081000104000198000014084201804000000040040000808000000008c020800423a192001814002021044200000009200004000402000008
>
> Is there are way to convert them to RDKit bitvector fingerprint objects or
> at least bitvector strings in python?
>
There is an rdkit cartridge function called bfp_to_binary_text() that you
can use for the bit vector fingerprints:
In [61]: m = Chem.MolFromSmiles('COC')
In [62]: fp =
Chem.RDKFingerprint(m,minPath=1,maxPath=6,fpSize=1024,nBitsPerHash=2)
In [63]: curs.execute("select bfp_to_binary_text(rdkit_fp('COC'))")
In [64]: row = curs.fetchone()
In [66]: nfp = DataStructs.CreateFromBinaryText(str(row[0]))
In [67]: nfp==fp
Out[67]: True
I don't think there's currently a way to do something equivalent for
count-based fingerprints (sfp's in the cartridge nomenclature), but it
could be added if there was demand.
-greg
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