/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package demo;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry;
import org.biojava.nbio.structure.symmetry.core.AxisAligner;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup;

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

/**
 * Created by ap3 on 02/04/2015.
 */
public class DemoOrientBioAssembly {

        public static void main(String[] args){


                //String[] pdbIDs = new String[]{"4HHB","4AQ5","1LTI","1STP","4F88","2W6E","2LXC","3OE7","4INU","4D8s","4EAR","4IYQ","3ZKR"};

                String[] pdbIDs = new String[]{"4x2s"};

                int bioAssemblyNr = 1;

                /*
                        Local symmetry

                        2WPD has 2 local symmetries.

                        Other examples with a single local symmetry are:
                        4F88 – local C8
                        1LTI – local C5
                        2W6E – local C3
                        2LXC – local C2
                        3OE7 – local C3

                        Local Pseudosymmetry, structure only

                        3ZDY
                        3ZDX

                        Helical

                        1B47

                 */

                for ( String pdbID : pdbIDs)
                {
                        try {

                                runPDB(pdbID,bioAssemblyNr);

                        } catch (Exception e) {
                                // TODO Auto-generated catch block
                                e.printStackTrace();
                        }
                }

        }

        public static void runPDB(String pdbID, int bioAssemblyNr) throws IOException, StructureException {



                pdbID = pdbID.toLowerCase();


                //Structure s = StructureIO.getBiologicalAssembly(pdbID, bioAssemblyNr);
                Structure s = readStructure(pdbID, bioAssemblyNr);

                QuatSymmetryParameters parameters = new QuatSymmetryParameters();
                parameters.setOnTheFly(true);
                parameters.setVerbose(true);


                CalcBioAssemblySymmetry calc = new CalcBioAssemblySymmetry(s, parameters);

                QuatSymmetryDetector detector = calc.orient();


                List<QuatSymmetryResults> globalResults = detector.getGlobalSymmetry();

                System.out.println("# of global results: " + globalResults.size());

                List<List<QuatSymmetryResults>> localResults = detector.getLocalSymmetries();



                showResults(s, pdbID + "[" + bioAssemblyNr + "] Global", globalResults);


                for (int counter = 0;counter < localResults.size() ; counter++){
                        List<QuatSymmetryResults> localResultsL = localResults.get(counter);

                        showResults(s,pdbID + "[" + bioAssemblyNr + "] Local #" + (counter+1) , localResultsL);
                }

                //determine default view:
                boolean defaultFound = false;

                for ( QuatSymmetryResults r : globalResults) {
                        System.out.println(r.getSymmetry());
                        //                      if (! r.getRotationGroup().getPointGroup().equals("C1")) {
                        //                              defaultResult = r;
                        //                              defaultFound = true;
                        //                      } else if ( r.getSubunits().isPseudoSymmetric()) {
                        //                              defaultResult = r;
                        //                              defaultFound  = true;
                        //                      }
                        if (r.isPreferredResult()) {

                                defaultFound = true;
                                System.out.println("!!!");
                        }

                }
                if ( ! defaultFound) {
                        for (List<QuatSymmetryResults> localResultSet : localResults) {
                                for ( QuatSymmetryResults r : localResultSet) {
                                        System.out.println(r.getSymmetry());
                                        if ( r.isPreferredResult()) {

                                        }
                                }
                        }
                }


        }

        private static void showResults(Structure s, String title,
                                                                        List<QuatSymmetryResults> results) {


                int count = 0 ;
                for (QuatSymmetryResults result: results) {

                        String longTitle = title + " count:"+ count + " [" + result.getSubunits().getStoichiometry() +"]";

                        String script = "set defaultStructureDSSP true; set measurementUnits ANGSTROMS;  select all;  spacefill off; wireframe off; " +
                                        "backbone off; cartoon on; color cartoon structure; color structure;  select ligand;wireframe 0.16;spacefill 0.5; " +
                                        "color cpk ; select all; model 0;set antialiasDisplay true; autobond=false;save STATE state_1;" ;
                        count++;

                        if ( result.getSubunits().isPseudoSymmetric()) {
                                longTitle += " pseudosymmetric!";
                        } else {
                                System.out.println(" not pseudosymmetric!");

                        }

                        AxisAligner aligner = AxisAligner.getInstance(result);

                        // use factory method to get point group specific instance of script generator
                        JmolSymmetryScriptGenerator scriptGenerator = JmolSymmetryScriptGeneratorPointGroup.getInstance(aligner, "g");

                        script += scriptGenerator.getOrientationWithZoom(0);
                        script += scriptGenerator.drawPolyhedron();
                        script += scriptGenerator.drawAxes();
                        script += scriptGenerator.colorBySymmetry();


                        longTitle += " M:" + result.getMethod();

                        longTitle += String.format(" SEQ: %.2f - %.2f", result.getSubunits().getMinSequenceIdentity() ,result.getSubunits().getMaxSequenceIdentity());





                        script += "draw axes* on; draw poly* on;";


                        // show in Jmol...

                        StructureAlignmentJmol jmol = new StructureAlignmentJmol();
                        jmol.setStructure(s);

                        jmol.setTitle(longTitle);
                        jmol.evalString(script);
                }


        }



        private static Structure  readStructure(String pdbId, int bioAssemblyId) {
                // initialize the PDB_DIR env variable
                AtomCache cache = new AtomCache();
                cache.setUseMmCif(true);

                FileParsingParameters params = new FileParsingParameters();
                params.setParseCAOnly(true);
                params.setAtomCaThreshold(Integer.MAX_VALUE);
                cache.setFileParsingParams(params);

                Structure structure = null;
                try {
                        structure = cache.getBiologicalAssembly(pdbId, bioAssemblyId);
                } catch (IOException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                } catch (StructureException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                }

                return structure;
        }
}