[Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction
Open-Source Cheminformatics and Machine Learning
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From: Taka S. <ser...@gm...> - 2016-07-25 13:44:37
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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 |