Tversky similarity for ECFP4 (JChem)

User 1617557bc2

16-10-2014 14:42:55

Dear support,

Is it possible to calculate the Tversky similarities for the ECFP4 or FCFP4 finger prints in JChem with the SimilarityCalculator class? is it possible to do it in another way in JChem? What Classes should I use if it is possible?

I can't get it to work but if works fine for the CFP finger print.


Best regards

Axel R

ChemAxon 5fc3e8d7d0

13-11-2014 13:12:57

Dear Axel,

Yes, it is possible.
See the following example code:

// create the calculator object
final SimilarityCalculator<int[]> calculator = SimilarityCalculatorFactory.create("TVERSKY;0.33;0.99");
// query, target molecules
final Molecule query = MolImporter.importMol("CC", "smiles");
final Molecule target = MolImporter.importMol("CC(=O)OC1=CC=CC=C1C(O)=O", "smiles");

// query, target fingerprints
final ECFP query_ecfp = new ECFP(new ECFPParameters());
final ECFP target_ecfp = new ECFP(new ECFPParameters());

// calculate similarity
final float similarity = calculator.getSimilarity(FPRetriever.getECFPFP(target_ecfp));

We also have a new Descriptor API, currently in Beta version, which can calculate Tversky similarity. If you would like to try it, please contact us by email:

Best regard,