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 ? ;-)