import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.smiles.SmilesParser;
import java.util.*;

public class CDKsim {
    public CDKsim() {};
    private  double getTanimotoCoefficient(BitSet fpp1, BitSet fpp2)
    {
	BitSet fp1 = (BitSet) fpp1.clone();
	BitSet fp2 = (BitSet) fpp2.clone();

	    int ntarget = fp1.cardinality();
        int nquery = fp2.cardinality();

        fp1.and(fp2);
        int ncommon = fp1.cardinality();

        double tanicoeff = (double)ncommon / (double)(nquery+ntarget-ncommon);
        return( tanicoeff );
    }

    public  double[] getSimMatrix(String[] mols, int length, int depth) throws CDKException {
        int nmol = mols.length;
	Fingerprinter fprinter = new Fingerprinter(length, depth);

        double[][] sm = new double[ nmol ][ nmol ];
        BitSet[] fparray = new BitSet[ nmol ];
        for (int i = 0; i < mols.length; i++) {
            IMolecule mol = null;
            SmilesParser sp = new SmilesParser();
            mol = sp.parseSmiles(mols[i]);
            if (mol == null) {
                throw new CDKException("SmilesParser exception");
            }
            if (length <= 0) length = 1204;
            if (depth < 0) depth = 6;
            try {
                fparray[i] = fprinter.getFingerprint(mol);
            } catch (Exception cdke) {
                throw new CDKException("Fingerprinter error");
            }
        }

        for (int i = 0; i < nmol-1; i++) {
            for (int j = i+1; j < nmol; j++) {
                sm[i][j] = getTanimotoCoefficient(fparray[i], fparray[j]);
                sm[j][i] = sm[i][j];
            }
        }
        for (int i = 0; i < nmol; i++) sm[i][i] = 1.0;
        double[] retval = new double[nmol*nmol];
        for (int i = 0; i < nmol; i++){
            String s = "";
            for (int j = 0; j < nmol; j++) {
                retval[i*nmol + j] = sm[i][j];
                s = s + sm[i][j]+" ";
            }
            System.out.println(s);
        }
        return(retval);
    }
    
    public double getSim(String target, String query, int length, int depth) throws CDKException {
	Fingerprinter fprinter = new Fingerprinter(length, depth);
        IMolecule mol1 = null;
        IMolecule mol2 = null;
        SmilesParser sp1 = new SmilesParser();
        SmilesParser sp2 = new SmilesParser();
        mol1 = sp1.parseSmiles(target);
        mol2 = sp2.parseSmiles(query);

        if (mol1 == null || mol2 == null) {
            throw new CDKException("SmilesParser exception");
        }
        if (length <= 0) length = 1204;
        if (depth < 0) depth = 6;

        BitSet fp1 = null;
        BitSet fp2 = null;

        try {
            fp1 = fprinter.getFingerprint(mol1);
            fp2 = fprinter.getFingerprint(mol2);
        } catch (Exception cdke) {
            throw new CDKException("Fingerprinter error");
        }


        int ntarget = fp1.cardinality();
        int nquery = fp2.cardinality();

        fp1.and(fp2);
        int ncommon = fp1.cardinality();

        double tanicoeff = (double)ncommon / (double)(nquery+ntarget-ncommon);
        return( tanicoeff );
    }

        
}