Greetings,
I have a question about morgan fingerprints. The code is pasted at the end
of the email, and please see the attached images for the results.
For valine molecule, the radius is set to be 2. The dictionary (atom index,
radius) shows all the substructures of all atoms with radius 0 as
fingerprints, and all the substructures of all the atoms with radius 1 as
fingerprints. But there are only a few substructures with radius 2 as
fingerprints. Why so few?
Thanks.
Best wishes,
Wendong
PS. The code is below:
m1 = Chem.MolFromSmiles('CC(C)[C@@H](C(=O)O)N')
di1 = {}
fp1 = AllChem.GetMorganFingerprintAsBitVect(m1, radius = 2, nBits = 2048,
bitInfo = di1)
tu1 = [(m1, x, di1) for x in fp1.GetOnBits()]
Draw.DrawMorganBits(tu1, molsPerRow = 4, legends=[str(x) for x in
fp1.GetOnBits()])
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