I am using Tanimoto dissimilarity function of yours in .NET platform to calculate similarity between two chemicals. Everything was perfectly fine, however I have realized something interesting when analyzing my data.
For the smiles codes given below with their PDB IDS, my code returns 1 as similarity score. (In other words 0 for dissimilarity score).
To my knowledge, similarity score is 1 when a chemical is only compared to itself. So I try to check similarity scores of the ligands given above in an online tool (http://chemmine.ucr.edu/) and similarity scores in there was like 0.5 or 0.6.
So this is an important issue for me, this project is important for my academic study. I will appreciate it a lt if you enlighten me!
Thanks in advance,
Here is my code;
CFParameters cfpConfig = new CFParameters();
string smiles1 = lg1.lSMILES;
string smiles2 = lg2.lSMILES;
ChemicalFingerprint cf1 = new ChemicalFingerprint(cfpConfig);
ChemicalFingerprint cf2 = new ChemicalFingerprint(cfpConfig);
return (1 - cf1.getTanimoto(cf2));