/*
 * 03/03/2006 - Added methods to provide MW and MF webservices
 *
 */
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 org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.tools.HydrogenAdder;

import java.util.*;
import java.io.*;

public class CDKws {
    public CDKws() {};

    public float getMolecularWeight(String s) throws CDKException {
	try {
	    SmilesParser sp = new SmilesParser();
	    IMolecule mol = sp.parseSmiles(s);
	    HydrogenAdder hAdder=new HydrogenAdder();
	    hAdder.addExplicitHydrogensToSatisfyValency(mol);
	    MFAnalyser mfa = new MFAnalyser(mol);
	    return(mfa.getCanonicalMass());
	} catch (CDKException cdke) {
	    throw new CDKException(cdke.toString());
	} catch (IOException ioe) {
	    throw new CDKException(ioe.toString());
	} catch (ClassNotFoundException cnfe) {
	    throw new CDKException(cnfe.toString());
	}
    }
    public String getMolecularFormula(String s) throws CDKException {
	try {
	    SmilesParser sp = new SmilesParser();
	    IMolecule mol = sp.parseSmiles(s);
	    HydrogenAdder hAdder=new HydrogenAdder();
	    hAdder.addExplicitHydrogensToSatisfyValency(mol);
	    MFAnalyser mfa = new MFAnalyser(mol);
	    return(mfa.getMolecularFormula());
	} catch (CDKException cdke) {
	    throw new CDKException(cdke.toString());
	} catch (IOException ioe) {
	    throw new CDKException(ioe.toString());
	} catch (ClassNotFoundException cnfe) {
	    throw new CDKException(cnfe.toString());
	}
    }
    public String getHTMLMolecularFormula(String s) throws CDKException {
	try {
	    SmilesParser sp = new SmilesParser();
	    IMolecule mol = sp.parseSmiles(s);
	    HydrogenAdder hAdder=new HydrogenAdder();
	    hAdder.addExplicitHydrogensToSatisfyValency(mol);
	    MFAnalyser mfa = new MFAnalyser(mol);
	    return(mfa.getHTMLMolecularFormula());
	} catch (CDKException cdke) {
	    throw new CDKException(cdke.toString());
	} catch (IOException ioe) {
	    throw new CDKException(ioe.toString());
	} catch (ClassNotFoundException cnfe) {
	    throw new CDKException(cnfe.toString());
	}
    }
	    
    public String getFingerprintString(String s) throws CDKException {
        String print = "";
        try {
            print = getFingerprintString(s, 1024, 6);
        } catch (CDKException cdke) {
            throw new CDKException("SmilesParser error");
        }
        return(print);
    }
    public String getFingerprintString(String s, int length) throws CDKException {
        String print = "";
        if (length <= 0) length = 1204;
        try {
        print = getFingerprintString(s,length,6);
        } catch (CDKException cdke) {
            throw new CDKException("SmilesParser error");
        }
        return(print);
    }
    public String getFingerprintString(String s, int length, int depth) throws CDKException {
        String print = "";
        IMolecule mol = null;
        SmilesParser sp = new SmilesParser();
        mol = sp.parseSmiles(s);
        if (mol == null) {
            throw new CDKException("SmilesParser exception");
        }
        if (length <= 0) length = 1204;
        if (depth < 0) depth = 6;
	Fingerprinter fprinter = new Fingerprinter(length, depth);
	try {
        print = fprinter.getFingerprint(mol).toString();
	} catch (Exception e) {
	    throw new CDKException("Fingerprinter error");
	}
        return(print);
    }
    

    public Vector getFingerprintVector(String s) throws CDKException {
        String fp;
        try {
            fp = getFingerprintString(s,1024,6);
        } catch (CDKException cdke) {
            throw new CDKException("SmilesParser error");
        }

        String[] st = fp.substring(1,fp.length()-1).split("[\\s,]");
        Vector v = new Vector();
        for (int i = 0; i < st.length; i++) {
            if (st[i].equals("")) continue;
            v.add( new Integer(st[i]) );
        }
        return(v);
    }
    public Vector getFingerprintVector(String s, int length) throws CDKException {
        String fp;
        if (length <= 0) length = 1204;
        try {
            fp = getFingerprintString(s,length,6);
        } catch (CDKException cdke) {
            throw new CDKException("SmilesParser error");
        }

        String[] st = fp.substring(1,fp.length()-1).split("[\\s,]");
        Vector v = new Vector();
        for (int i = 0; i < st.length; i++) {
            if (st[i].equals("")) continue;
            v.add( new Integer(st[i]) );
        }
        return(v);
    }
    public Vector getFingerprintVector(String s, int length, int depth) throws CDKException {
        IMolecule mol = null;
        SmilesParser sp = new SmilesParser();
        mol = sp.parseSmiles(s);
        if (mol == null) {
            throw new CDKException("SmilesParser exception");
        }
        if (length <= 0) length = 1204;
        if (depth < 0) depth = 6;
	Fingerprinter fprinter = new Fingerprinter(length, depth);
	String fp = null;
	try {
	    fp = fprinter.getFingerprint(mol).toString();
	} catch (Exception e) {
	    throw new CDKException("Fingerprinter error");
	}
        String[] st = fp.substring(1,fp.length()-1).split("[\\s,]");
        Vector v = new Vector();
        for (int i = 0; i < st.length; i++) {
            if (st[i].equals("")) continue;
            v.add( new Integer(st[i]) );
        }
        return(v);
    }
        
}