I want to differentiate between two similar molecules (SMILES pasted below) using Tanimoto and Euclidean methods. I have tried various fingerprinting parameters. However, both dissimilarity scores always amount to 0, meaning the two molecules cannot be differentiated computationally. Can the technical support please provide some advice? Thank you in advance!
Here are the settings I have tried:
ChemAxon version: 5.9
Fingerprint length: 128, 256, 512, and 1024
Maximum pattern length: 7 and 8
Bits to be set for patterns: 2 and 3
Two molecules to be distinguished:
The fingerprints were generated using the code (new MolHandler(molecule1)).generateFingerprintInInts(param1, param2, param3)