[Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

[Taka S. <ser...@gm...>]

Dear rdkitters,
I want to analyse and build prediction model about reaction or matched
molecular pair ( molecular transformations ).

I found new function named CreateDifferenceFingerprintForReaction. So, I
tried to use the function to do it. But I confused following result.

I defined three reactions that transform C to N.
I expected that tanimoto similarity would be same but Tanimoto similarity
of the reactions were quite different. I confused these result.
My code is following....
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import rdBase
from rdkit.Chem import rdChemReactions
from rdkit.Chem import DataStructs

rdBase.rdkitVersion =>'2016.03.1'

rxn1 = AllChem.ReactionFromSmarts( '[C:1]C1CCCCC1>>[N:1]C1CCCCC1' )

rxn2 = AllChem.ReactionFromSmarts( '[C:1]C1CCCNC1>>[N:1]C1CCCNC1' )

rxn3 = AllChem.ReactionFromSmarts( '[C:1]c1ccccc1>>[N:1]c1ccccc1' )

rxfp1 = rdChemReactions.CreateDifferenceFingerprintForReaction(rxn1)

rxfp2 = rdChemReactions.CreateDifferenceFingerprintForReaction(rxn2)

rxfp3 = rdChemReactions.CreateDifferenceFingerprintForReaction(rxn3)

tc12 = DataStructs.TanimotoSimilarity(rxfp1, rxfp2)

tc13 = DataStructs.TanimotoSimilarity(rxfp1, rxfp3)

tc23 = DataStructs.TanimotoSimilarity(rxfp2, rxfp3)

print( tc12,tc13, tc23 )

# I got following score. Why 2nd and 3rd similarity was zero?

0.7142857142857143 0.0 0.0

Any advice and suggestions will be greatly appreciated
Best regards,
Takayuki