Hi RDKit,
How does one input the number of bits to the ShapeTanimotoDist function?
The docs indicate the default is
*rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE,
*but I tried some other values and this gave unexpected results.
Specifically: when increasing to higher bit values, the tanimoto similarity
gets quite small, whereas I assumed increasing the sampled bits would
simply improve the precision of the calculation.
example:
from rdkit import Chem
from rdkit.DataStructs import TWOBITVALUE, FOURBITVALUE, EIGHTBITVALUE
from rdkit.Chem.rdShapeHelpers import ShapeTanimotoDist
testmol = Chem.MolFromSmiles('CCCC')
testmolH = Chem.AddHs(testmol)
AllChem.EmbedMultipleConfs(testmolH, 2)
for bits in [TWOBITVALUE, FOURBITVALUE, EIGHTBITVALUE]:
print(ShapeTanimotoDist(testmolH, testmolH, 0,1,bitsPerPoint=bits))
output:
0.38089171974522296
0.14635701022642242
0.00452852989652238
Thanks!
Lewis
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