Tversky similarity for ECFP4 (JChem)

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

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());

query_ecfp.generate(query);

final ECFP target_ecfp = new ECFP(new ECFPParameters());

target_ecfp.generate(target);

		

// calculate similarity

calculator.setQueryFingerprint(FPRetriever.getECFPFP(query_ecfp));

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: disco-support_at_chemaxon.com

Best regard,
Laszlo