Good morning,
Use this class for Tanimoto calucations:
org.openscience.cdk.similarity.Tanimoto (see doc:
http://cdk.github.io/cdk/latest/docs/api/index.html)
you could do something like this to calculate your tanimoto score:
public static double cdkCalculateTanimotoCoef(IFingerprinter fingerprinter,
IAtomContainer acReference, IAtomContainer acStructure ) {
double ret = 0.0;
try {
IBitFingerprint fpReference =
fingerprinter.getBitFingerprint(acReference);
//Tanimoto-score
IBitFingerprint fpStructure =
fingerprinter.getBitFingerprint(acStructure);
ret = Tanimoto.calculate(fpReference, fpStructure);
} catch (Exception ex) {
//...
}
return ret;
}
Viele Grüße,
Manuel Stesycki
IT
0208 / 306-2146
Physikbau, Büro 117
[email protected]<mailto:[email protected]>
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
D-45470 Mülheim an der Ruhr
http://www.kofo.mpg.de/de
Am 24.03.2021 um 04:55 schrieb Sub Jae Shin
<[email protected]<mailto:[email protected]>>:
To CDK developers.
Hello, I'm trying to get drug-drug similarity by Tanimoto score.
I'm a beginner of cdk and java, so I'm stuck in the process of changing smiles
file to Tanimoto score's calculate method's variable.
package com.company;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.SMILESReader;
import java.io<http://java.io>.*;
public class Main {
public static void main(String[] args) {
try {
InputStream mol2DataStream = new
FileInputStream("../data/drugbank/structure.smiles");
SMILESReader reader = new SMILESReader(mol2DataStream);
IChemFile file = reader.read(new ChemFile());
} catch (FileNotFoundException | CDKException e) {
System.out.println(e.getMessage());
}
}
}
Sincerely
Seopjae Shin.
_______________________________________________
Cdk-user mailing list
[email protected]<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/cdk-user
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
