I have a fragment of code generating fingerprints for a long list of molecules
(length ~ 1000)
for index in range(0,len(smi)):
smiles=smi[index]
mol=Chem.MolFromSmiles(smiles)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
dm = Chem.Get3DDistanceMatrix(mol)
fp = Generate.Gen2DFingerprint(mol,factory, dMat=dm)
fp = fp.ToBitString()
bs[index]=fp
The length of each bitvectors generated is 39972, and the list has a lot of
redundant '1's and '0's.
Is there an easy method to filter out these redundant bits?
Cheers,
Steve.
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