package smsdcmd.examples;

import java.io.File;
import java.io.FileInputStream;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.smsd.SMSD;
import org.openscience.cdk.smsd.interfaces.IMCS.Algorithm;
import org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator;
import org.openscience.cdk.smsd.tools.MDLFileReader;


/*
 * This example file covers the MCS search part of the SMSD.
 * A result is obtained if query and template structure has atleast one common MCS.
 * Query molecule is always the first molecule and template is the second molecule.
 * Use the isSubgraph() method to find if query is a subgraph/substructure of the template mol.
 *
 *
 *
 * MCSSearch.java
 * @modified 3 March, 2010, 11.06 AM
 *
 * @author Syed Asad Rahman, EMBL-EBI, Cambridge, UK
 * contact asad@ebi.ac.uk
 *
 */
public class MCSSearch {

    /** Creates a new instance of SMSD */
    public MCSSearch() {
    }

    /**
     * @param args the command line arguments
     * @throws Exception
     */
    public static void main(String[] args) throws Exception {
        try {

            String mol1 = "Data/ATP.mol";
            String mol2 = "Data/ADP.mol";

            boolean first_MCS = false;

            boolean exists = (new File(mol1)).exists();
            if (!exists) {

                System.err.println("Error: The Assigned File Path is not Correct " + mol1);
                System.exit(1);
            }

            exists = (new File(mol2)).exists();
            if (!exists) {

                System.err.println("Error: The Assigned File Path is not Correct " + mol2);
                System.exit(1);
            }

            MDLFileReader R1 = new MDLFileReader(new FileInputStream(mol1));
            IMolecule A1 = R1.getMolecule();

            MDLFileReader R2 = new MDLFileReader(new FileInputStream(mol2));
            IMolecule A2 = R2.getMolecule();

            ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(A1);
            ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(A2);

            A1 = (IMolecule) ExtAtomContainerManipulator.removeHydrogensAndPreserveAtomID(A1);
            A2 = (IMolecule) ExtAtomContainerManipulator.removeHydrogensAndPreserveAtomID(A2);

//	Calling the main algorithm to perform MCS cearch

            CDKHueckelAromaticityDetector.detectAromaticity(A1);
            CDKHueckelAromaticityDetector.detectAromaticity(A2);

            boolean bondSensitive = true;
            boolean removeHydrogen = true;
            boolean stereoMatch = true;
            boolean fragmentMinimization = true;
            boolean energyMinimization = true;

            SMSD comparison = new SMSD(Algorithm.DEFAULT, bondSensitive);
            comparison.init(A1, A2, removeHydrogen);
            comparison.setChemFilters(stereoMatch, fragmentMinimization, energyMinimization);

//      Get modified Query and Target Molecules as Mappings will correspond to these molecules
            IAtomContainer Query = comparison.getReactantMolecule();
            IAtomContainer Target = comparison.getProductMolecule();

            //Print all MCS solutions if first_MCS is false
            if (first_MCS == false) {
                int count_final_sol = 1;
                System.out.println("Output of the final Mappings: ");
                try {
                    if (comparison.getAllMapping() != null) {
                        for (Map<Integer, Integer> final_solution : comparison.getAllMapping()) {
                            int final_solution_size = final_solution.size();
                            System.out.println("Final mapping Nr. " + ++count_final_sol + " Size:" + final_solution_size);

                            for (Map.Entry<Integer, Integer> mapping : final_solution.entrySet()) {
                                System.out.println((mapping.getKey() + 1) + " " + (mapping.getValue() + 1));

                                //Get the mapped atom number in Query Molecule
                                int queryMappingNumber = mapping.getKey();
                                //Get the mapped atom number in Target Molecule
                                int targetMappingNumber = mapping.getValue();

                                //Get the mapped atom in Query Molecule
                                IAtom queryAtom = Query.getAtom(queryMappingNumber);
                                //Get the mapped atom in Target Molecule
                                IAtom targetAtom = Target.getAtom(targetMappingNumber);
                                //Print mapped atom numbers
                                System.out.println(queryMappingNumber + " "
                                        + (targetMappingNumber));
                                //Print mapped atoms
                                System.out.println(queryAtom.getSymbol() + " "
                                        + targetAtom.getSymbol());
                            }
                            System.out.println("");

                            System.out.println("Stereo Match: " + comparison.getStereoScore(count_final_sol - 1));
                            System.out.println("Stereo different: " + comparison.isStereoMisMatch());
                            System.out.println("Fragment Size: " + comparison.getFragmentSize(count_final_sol - 1));
                            System.out.println("Tanimoto Similarity Score: " + comparison.getTanimotoSimilarity());
                            System.out.println("Tanimoto Euclidean Distance: " + comparison.getEuclideanDistance());
                            count_final_sol++;

                        }

                        System.out.println("");
                    }
                } catch (Exception ex) {
                    ex.printStackTrace();
                }
            }





            //Output only first solution
            if (first_MCS) {
                try {


                    for (Map.Entry<Integer, Integer> mappings : comparison.getFirstMapping().entrySet()) {
                        //Get the mapped atom number in Query Molecule
                        int queryMappingNumber = mappings.getKey();
                        //Get the mapped atom number in Target Molecule
                        int targetMappingNumber = mappings.getValue();

                        //Get the mapped atom in Query Molecule
                        IAtom queryAtom = Query.getAtom(queryMappingNumber);
                        //Get the mapped atom in Target Molecule
                        IAtom targetAtom = Target.getAtom(targetMappingNumber);
                        //Print mapped atom numbers
                        System.out.println(queryMappingNumber + " "
                                + (targetMappingNumber));
                        //Print mapped atoms
                        System.out.println(queryAtom.getSymbol() + " "
                                + targetAtom.getSymbol());
                    }
                    System.out.println("");

                    System.out.println("");

                    System.out.println("Stereo Match: " + comparison.getStereoScore(0));
                    System.out.println("Stereo different: " + comparison.isStereoMisMatch());
                    System.out.println("Fragment Size: " + comparison.getFragmentSize(0));
                    System.out.println("Tanimoto Similarity Score: " + comparison.getTanimotoSimilarity());
                    System.out.println("Tanimoto Euclidean Distance: " + comparison.getEuclideanDistance());
                    System.out.println("");
                } catch (Exception ex) {
                    ex.printStackTrace();
                }
                System.out.println("");
            }
            System.out.println("");


            System.out.println("");

        } catch (Exception ex) {
            Logger.getLogger(SMSDExample.class.getName()).log(Level.SEVERE, null, ex);
        }


    }

    /**
     *
     * @param Molecule1
     * @param Molecule2
     */
    private static void printMolecules(IAtomContainer Molecule1, IAtomContainer Molecule2) {

        System.out.println("Molecule 1");

        for (int i = 0; i < Molecule1.getAtomCount(); i++) {

            System.out.print(Molecule1.getAtom(i).getSymbol() + " ");
        }

        System.out.println();
        System.out.println("Molecule 2");
        for (int i = 0; i < Molecule2.getAtomCount(); i++) {

            System.out.print(Molecule2.getAtom(i).getSymbol() + " ");
        }
        System.out.println();

    }
}