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Tversky similarity for ECFP4 (JChem)
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Axel

Joined: 12 Feb 2013
Posts: 1

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Link to postPosted: Thu Oct 16, 2014 3:42 pmPost subject: Tversky similarity for ECFP4 (JChem) Reply with quote

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

László
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Joined: 14 Jan 2011
Posts: 78

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Link to postPosted: Thu Nov 13, 2014 2:12 pmPost subject: Reply with quote

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 

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