QED calculation on RDKit 2017.09 #RDKit

QED (quantitative estimate of drug-likeness ) is an one of score of drug likeness reported by Hopkins group.

The author provided QED calculator for pipeline pilot. So QED could not calculate without pipeline pilot.
But, now we can calculate QED by using RDKit!
RDKit 201709 was implemented QED descriptor. Seems good, let’s use the function.
It is very simple. Just call qed!. I used dataset the same as yesterday.

import os
from rdkit.Chem import rdBase, RDConfig
from rdkit import Chem
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem.Descriptors import qed
print( rdBase.rdkitVersion )

sdfpath = os.path.join( RDConfig.RDDocsDir, "Book/data/cdk2.sdf" )
mols = [ m for m in Chem.SDMolSupplier( sdfpath ) if m != None ]
df = PandasTools.LoadSDF( sdfpath )
print( len( mols ))

df.head( 2 )

df[ "QED" ] =  df.ROMol.apply( qed )
df.head(2 )

from rdkit.Chem import QED
for mol in mols:
    print( QED.properties( mol ) )

It is easy isn’t it ?
I pushed sample code to my repository.
By the way, original QED score was based on ChEMBL ver 09. So, dataset is old. Does the score show difference when we use new version of ChEMBL ? ;-)


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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