Dear all,
Working in an example I realized that there are at least two ways of
computing morgan fingerprints for a molecule using rdkit. But using the
exact same properties in both ways I get different vectors. Am I missing
something?
First approach:
info = {}
mol = Chem.MolFromSmiles('C/C1=C\\C[C@H]([C+](C)C)CC/C(C)=C/CC1')
fp = AllChem.GetMorganFingerprintAsBitVect(mol, useChirality=True,
radius=2, nBits = 124, bitInfo=info)
vector = np.array(fp)
vector
array([0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1])
Second approach:
morgan_fp_gen =
rdFingerprintGenerator.GetMorganGenerator(includeChirality=True, radius=2,
fpSize=124)
mol = Chem.MolFromSmiles('C/C1=C\\C[C@H]([C+](C)C)CC/C(C)=C/CC1')
fp = morgan_fp_gen.GetFingerprint(mol)
vector = np.array(fp)
vector
array([0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0,
1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0])
Which are clearly different, even using chirality in both cases.
Besides, is there a way to get the bitInfo from a bit vector using the
second approach?. This means if there is a way to get the bitInfo
dictionary from a bit vector created using a generator as in the second
approach. Cause as far as I know what you can get is the info corresponding
to 1 in the vector using fp.GetOnBits() but that does not include the atom
position
Best regards,
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