Hi Lewis,
This looks odd to me as well, but I don't have a quick answer to
explain/account for it.
I'll try and take a look in the near future.
-greg
On Wed, Jul 21, 2021 at 11:57 PM Lewis Martin <lewis.marti...@gmail.com>
wrote:
> 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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