How to create FCFP object?

I want to use FCFP fingerprint to calculate tanimoto score.  I managed to create a ECFP object (see below), and call ECFP.getTanimoto method.

            ECFPParameters ep = new ECFPParameters();
            ep.setLength(1024);
            ep.setDiameter(4);
            ep.setKeepCounts(false);
            ECFP Fp = new ECFP(ep);
            ECFPGenerator GenECFP = new ECFPGenerator();
            Molecule M = m.GetMolecule();
            string[] k1 = GenECFP.generate(M, Fp);

I didn't figure out how to put FCFP parametes(see below) into ECFPParameters.

Could you provide an example code to get a FCFP object?

Thanks

Bin

Hi Bin,

The easiest solution is to store your configuration in a separate XML file. E.g. you can start with downloading the FCFP example file from the ECFP/FCFP user guide:
http://www.chemaxon.com/jchem/examples/config/fcfp.xml

Once you have this file next to your code, you have to pass it to the ECFPParamaters constructor call:

ECFPParameters ep = new ECFPParameters(new File(pathToTheXmlConfigFile));

or if you have the content of the file as a String value in your code, you can also pass it to the constructor:

ECFPParameters ep = new ECFPParameters(xmlConfigString));

Note that the XML file or the XML string you use should be a full ECFP configuration, not only the IdentifierConfiguration part of it. You can use the example file linked above as a baseline.

Regards,
Peter