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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss