Hi Pavel,
On Wed, Apr 26, 2017 at 8:41 AM, Pavel Polishchuk <pavel_polishc...@ukr.net>
wrote:
> Hello,
>
> is it possible to store custom fingerprints in psql DB and use them
> for similarity search? And how to do this?
>
That's a great question and it took me a bit to get the answer working.
Since the answer isn't completely trivial and since it may be useful to
others, it seems like a good topic for an RDKit blog post. Those take a
while to write, but I've got an early version that lacks most of the
explanatory text up here:
https://github.com/greglandrum/rdkit_blog/blob/master/notebooks/Custom%20fingerprint%20in%20PostgreSQL.ipynb
I hope this helps,
-greg
> 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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