package pl.org.ptbi;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import org.biojava.bio.structure.Atom;
import org.biojava.bio.structure.Calc;
import org.biojava.bio.structure.Chain;
import org.biojava.bio.structure.Group;
import org.biojava.bio.structure.SVDSuperimposer;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.io.PDBFileReader;

public class Main {
    public static void main(String[] args) {
        PDBFileReader reader = new PDBFileReader();
        reader.setAutoFetch(true);
        reader.setPath(System.getProperty("java.io.tmpdir"));

        try {
            Structure left = reader.getStructureById("1EHZ");
            Structure right = reader.getStructureById("1EVV");

            List<Atom> listLeft = getPhosphorus(left.getChainByPDB("A"));
            List<Atom> listRight = getPhosphorus(right.getChainByPDB("A"));

            Atom[] atomSet1 = listLeft.toArray(new Atom[listLeft.size()]);
            Atom[] atomSet2 = listRight.toArray(new Atom[listRight.size()]);
            SVDSuperimposer superimposer = new SVDSuperimposer(atomSet1, atomSet2);
            Calc.rotate(right, superimposer.getRotation());
            Calc.shift(right, superimposer.getTranslation());

            double rmsd = SVDSuperimposer.getRMS(atomSet1, atomSet2);
            System.out.println(rmsd);
        } catch (IOException | StructureException e) {
            e.printStackTrace();
        }
    }

    private static List<Atom> getPhosphorus(Chain chain) {
        List<Atom> list = new ArrayList<>();

        for (Group group : chain.getAtomGroups()) {
            try {
                Atom atom = group.getAtom("P");
                list.add(atom);
            } catch (StructureException e) {
                System.err.println(e.getMessage());
            }
        }
        return list;
    }
}