Evaluate fingerprint accuracy ...

FPAccuracy.java

package net.sf.cdk.tools;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.ExtendedFingerprinter;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.fingerprint.FingerprinterTool;
import org.openscience.cdk.fingerprint.IFingerprinter;
import org.openscience.cdk.fingerprint.GraphOnlyFingerprinter;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.smiles.SmilesParser;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.BitSet;

/**
 * Testing accuracy of CDK fingerprints.
 *
 * @author Rajarshi Guha
 */
public class FPAccuracy {
    SmilesParser sp;

    public FPAccuracy() {
        sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    }

    private IAtomContainer getMolecule(String smi) throws CDKException {
        IAtomContainer frag = sp.parseSmiles(smi);
        CDKHueckelAromaticityDetector.detectAromaticity(frag);
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag);
        return frag;
    }

    private void process(IFingerprinter fp, String ofile) throws IOException, CDKException {
        BufferedReader reader = new BufferedReader(new FileReader("/Users/guhar/work/cdkfp/small_molecule-std.fragments2"));
        BufferedWriter writer = new BufferedWriter(new FileWriter(ofile));

        String line;
        int n = 0;
        while ((line = reader.readLine()) != null) {
            String[] toks = line.trim().split("\\s+");
            String fragsmi = toks[0];
            String parentsmi = toks[1];

            BitSet frag = fp.getFingerprint(getMolecule(fragsmi));
            BitSet parent = fp.getFingerprint(getMolecule(parentsmi));
            boolean issubset = FingerprinterTool.isSubset(parent, frag);
            writer.write(issubset+"\n");

            n++;
            if (n % 100 == 0) {
                System.out.print("Processed "+n+"\n");
            }
        }
        writer.close();
        reader.close();
    }

    private void checkStandard() throws IOException, CDKException {
        IFingerprinter fp = new Fingerprinter();
        process(fp, "/Users/guhar/fpacc.std");
    }

    private void checkExtended() throws IOException, CDKException {
        IFingerprinter fp = new ExtendedFingerprinter();
        process(fp, "/Users/guhar/fpacc.ext");
    }

    private void checkGraphOnly() throws IOException, CDKException {
        IFingerprinter fp = new GraphOnlyFingerprinter();
        process(fp, "/Users/guhar/fpacc.graph");
    }

    public static void main(String[] args) throws IOException, CDKException {
        FPAccuracy fpa = new FPAccuracy();
        fpa.checkExtended();
    }
}