import net.guha.util.cdk.ViewMolecule2D;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.mcss.RMap;
import org.openscience.cdk.smiles.SmilesParser;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

/**
 * @author Rajarshi Guha
 */
public class NoMCSS {


    NoMCSS() {
    }

    private IAtomContainer getMCSS(IAtomContainer mol1, IAtomContainer mol2) throws CDKException {
        IAtomContainer mcss = null;
        int maxac = -999;
        List ssList = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
        for (Object aSsList : ssList) {
            IAtomContainer ss = (IAtomContainer) aSsList;
            if (ss.getAtomCount() > maxac) {
                mcss = ss;
                maxac = ss.getAtomCount();
            }
        }
        return mcss;
    }

    public IMoleculeSet getUncommon(IAtomContainer mol, IAtomContainer mcss) throws CDKException {
        ArrayList<Integer> atomSerialsToDelete = new ArrayList<Integer>();

        List matches = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol, mcss);
        List mapList = (List) matches.get(0);
        for (Object o : mapList) {
            RMap rmap = (RMap) o;
            atomSerialsToDelete.add(rmap.getId1());
        }

        // at this point we have the serial numbers of the bonds to delete
        // we should get the actual bonds rather than delete by serial numbers
        ArrayList<IAtom> atomsToDelete = new ArrayList<IAtom>();
        for (Integer serial : atomSerialsToDelete) {
            atomsToDelete.add(mol.getAtom(serial));
        }

        // now lets get rid of the bonds themselves
        for (IAtom atom : atomsToDelete) {
            mol.removeAtomAndConnectedElectronContainers(atom);
        }

        // now we probably have a set of disconnected components
        // so lets get a set of individual atom containers for
        // corresponding to each component
        return ConnectivityChecker.partitionIntoMolecules(mol);
    }

    public static void main(String[] args) throws CDKException {
        String smi1 = "CSC1CC1NC";
        String smi2 = "C1CC1CCC";

        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer mol1 = sp.parseSmiles(smi1);
        IAtomContainer mol2 = sp.parseSmiles(smi2);

        NoMCSS nomcss = new NoMCSS();
        IAtomContainer mcss = nomcss.getMCSS(mol1, mol2);

        IMoleculeSet remainder1 = nomcss.getUncommon(mol1, mcss);
        System.out.println("remainder1.getMoleculeCount() = " + remainder1.getMoleculeCount());
        IMoleculeSet remainder2 = nomcss.getUncommon(mol2, mcss);
        System.out.println("remainder2.getMoleculeCount() = " + remainder2.getMoleculeCount());

        /*
        Iterator<IAtomContainer> mols = remainder1.molecules();
        while (mols.hasNext()) {
            IAtomContainer container = mols.next();
            ViewMolecule2D viewer = new ViewMolecule2D(container);            
            viewer.draw();
        }
        */


    }
}