Hello,
is it possible to store custom fingerprints in psql DB and use them
for similarity search? And how to do this?
I foundtwo commands bfp_to_binary_text(bfp) and
bfp_from_binary_text(bytea)in RDKit cartridge but cannot understand how
to use them.
I want to store pharmacophore fingerprints. There is no a built-in
command in RDKit cartridge to calculate them so I have to calculate them
in a Pythonscript. Then I need to store them in psql DB and create
similarity search index but I could not find a solution yet.
It might be of general interest how to store and use arbitrary
fingerprints in DB.
An example of pharmacophore FP generation:
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem.Pharm2D import Generate
import os
fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef')
factory = ChemicalFeatures.BuildFeatureFactory(fdefName)
sigFactory = SigFactory(factory, minPointCount=2, maxPointCount=3,
trianglePruneBins=False)
sigFactory.SetBins([(0,2),(2,5),(5,8)])
sigFactory.Init()
mol = Chem.MolFromSmiles('Cc1nc(CN(C)c2ncnc3ccc(-c4ccc5c(c4)OCO5)cc23)cs1')
fp = Generate.Gen2DFingerprint(mol, sigFactory)
Pavel.
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