3d conformer fingerprint calculation using RDKit # RDKit

Recently, attractive article was published in ACS journal.
The article describes how to calculate 3D structure based fingerprint and compare some finger prints that are well known in these area.
New method called “E3FP” is algorithm to calculate 3D conformer fingerprint like Extended Connectivity Fingerprint(ECFP). E3FP encodes information only atoms that are connected but also atoms that are not connected.

The author showed several examples. Very similar in 2D but not similar in 3D and vice versa.
Also compare E3FP similarity and ROCS score( TANIMOTO COMBO ) and showed good performance.
I was interested in the fingerprint. Fortunately, the author published the code in Anaconda cloud!!!!!!!
Install it and use it ASAP. ;-D
I am mac user, so installation is very very very easy! Just type.
I found some tips to use the package.
At first, molecules need _Name property to perform calculation.
Second, mol_from_sdf can read molecule from sdf but the function can not read sdf that has multiple molecules. So, I recommend to use molecule list instead of SDF.

conda install -c sdaxen sdaxen_python_utilities
conda install -c keiserlab e3fp

I used CDK2.sdf for test.
E3FP calculates unfolded finger print. But it can convert folded fingerprint and rdkit fingerprint using flod and to_rdkit function.

%matplotlib inline
import pandas as pd
import numpy as np
from rdkit import Chem
from e3fp.fingerprint.generate import fp, fprints_dict_from_mol
from e3fp.conformer.generate import generate_conformers
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from rdkit.Chem import DataStructs
from rdkit.Chem import AllChem
# this sdf has 3D conformer, so I do not need to generate 3D conf.
mols = [ mol for mol in Chem.SDMolSupplier( "cdk2.sdf", removeHs=False ) ]
fpdicts = [ fprints_dict_from_mol( mol ) for mol in mols ]
# get e3fp fingerprint
# if molecule has multiple conformers the function will generate multiple fingerprints.
fps = [ fp[5][0] for fp in fpdicts]
# convert to rdkit fp from e3fp fingerprint
binfp = [ fp.fold().to_rdkit() for fp in fps ]
# getmorganfp
morganfp = [ AllChem.GetMorganFingerprintAsBitVect(mol,2) for mol in mols ]

# calculate pair wise TC
df = {"MOLI":[], "MOLJ":[], "E3FPTC":[], "MORGANTC":[],"pairidx":[]}
for i in range( len(binfp) ):
    for j in range( i ):
        e3fpTC = DataStructs.TanimotoSimilarity( binfp[i], binfp[j] )
        morganTC = DataStructs.TanimotoSimilarity( morganfp[i], morganfp[j] )
        moli = mols[i].GetProp("_Name")
        molj = mols[j].GetProp("_Name")
        df["MOLI"].append( moli )
        df["MOLJ"].append( molj )
        df["E3FPTC"].append( e3fpTC )
        df["MORGANTC"].append( morganTC )
        df["pairidx"].append( str(i)+"_vs_"+str(j) )

The method is fast and easy to use. Bottle neck is how to generate suitable conformer(s).
Readers who interested in the package, please check the authors article.

I pushed my sample code to my repo.


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