// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.algorithms.misc;
  
  import ffx.algorithms.AlgorithmListener;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.AminoAcidUtils;
  import ffx.potential.bonded.AminoAcidUtils.AminoAcid3;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.Rotamer;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.potential.parsers.PDBFilter;
  
  import java.io.BufferedWriter;
  import java.io.File;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.Arrays;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  import java.util.regex.Matcher;
  import java.util.regex.Pattern;
  
  import static java.lang.String.format;
  
  /**
   * The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino
   * acids) for a Residue.
   *
   * @author Jacob M. Litman
   * @author Michael J. Schnieders
   */
  public class GenerateRotamers {
  
    private static final Logger logger = Logger.getLogger(GenerateRotamers.class.getName());
    private static final Pattern atRangePatt = Pattern.compile("(\\d+)-(\\d+)");
    private final Residue residue;
    private final int nChi;
    private final double[] currentChi;
    private final File outFile;
    private final MolecularAssembly molecularAssembly;
    private final AlgorithmListener listener;
    private final RotamerLibrary library;
    private final Potential potential;
    private double[] x;
    private AminoAcid3 baselineAAres;
    private Rotamer[] baselineRotamers;
    private double incr = 10.0; // Degrees to rotate each torsion by.
    private boolean aroundLibrary = false;
    private double width = 180.0; // Left 180 + right 180 = 360 degree coverage.
    private int startDepth = 0;
    private int endDepth;
    private boolean print = false; // If true, log energy at each torsion.
    private int nEval = 0;
    private boolean writeVideo = false;
    private File videoFile;
    private PDBFilter videoFilter;
  
    /**
     * Intended to create rotamer sets for nonstandard amino acids.
     *
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    * @param potential a {@link ffx.numerics.Potential} object.
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @param file Output file
    * @param nChi Number of rotameric torsions in the residue
    * @param listener a {@link ffx.algorithms.AlgorithmListener} object.
    */
   public GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue,
       File file, int nChi, AlgorithmListener listener) {
     this(molecularAssembly, potential, residue, file, nChi, listener,
         RotamerLibrary.getDefaultLibrary());
   }
 
   /**
    * Intended to create rotamer sets for nonstandard amino acids.
    *
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    * @param potential a {@link ffx.numerics.Potential} object.
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @param file Output file
    * @param nChi Number of rotameric torsions in the residue
    * @param listener a {@link ffx.algorithms.AlgorithmListener} object.
    * @param library Rotamer library to use
    */
   public GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue,
       File file, int nChi, AlgorithmListener listener, RotamerLibrary library) {
     this.residue = residue;
     this.nChi = nChi;
     endDepth = nChi - 1;
     this.potential = potential;
     this.molecularAssembly = molecularAssembly;
     this.listener = listener;
     this.currentChi = new double[nChi];
     this.library = library;
     Arrays.fill(currentChi, 0.0);
     File outputFile = file;
     if (outputFile.exists()) {
       String outName = outputFile.getName();
       for (int i = 1; i < 1000; i++) {
         outputFile = new File(format("%s_%d", outName, i));
         if (!outputFile.exists()) {
           break;
         }
       }
       if (outputFile.exists()) {
         logger.severe(format(" Could not version file %s", outName));
       }
     }
     outFile = outputFile;
     this.baselineAAres = residue.getAminoAcid3();
     baselineRotamers = library.getRotamers(baselineAAres);
   }
 
   /**
    * Accessory method for more simplistic saving of specific torsion states.
    *
    * @param torSets an array of {@link java.lang.String} objects.
    */
   public void applyAndSaveTorsions(String[] torSets) {
     for (String torSet : torSets) {
       String[] torsions = torSet.split(",");
       double[] values = new double[nChi * 2];
       Arrays.fill(values, 0.0);
       for (int i = 0; i < (Math.min(torsions.length, nChi)); i++) {
         double chival = Double.parseDouble(torsions[i]);
         currentChi[i] = chival;
         values[2 * i] = chival;
       }
       Rotamer newRot = generateRotamer(values);
       RotamerLibrary.applyRotamer(residue, newRot);
       writeSnapshot();
     }
   }
 
   /**
    * Sets a standard amino acid to be the baseline for rotamer generation. For example, use TYR as a
    * baseline for phospho-tyrosine.
    *
    * @param aa3 a {@link AminoAcid3} object.
    */
   public void setBaselineAARes(AminoAcid3 aa3) {
     this.baselineAAres = aa3;
     if (aa3 == AminoAcidUtils.AminoAcid3.UNK) {
       boolean orig = library.getUsingOrigCoordsRotamer();
       library.setUseOrigCoordsRotamer(false);
       baselineRotamers = residue.setRotamers(library);
       library.setUseOrigCoordsRotamer(orig);
     } else {
       baselineRotamers = library.getRotamers(aa3);
     }
     aroundLibrary = true;
   }
 
   /**
    * Set which torsions to work on. Negative end values set the final depth to be the total number of
    * torsions.
    *
    * @param start The first torsion to work on.
    * @param end The last torsion to work on.
    */
   public void setDepth(int start, int end) {
     startDepth = start;
     if (end < 1 || end > nChi) {
       endDepth = nChi - 1;
     } else {
       endDepth = end;
     }
   }
 
   /**
    * Inactivates electrostatics for atom sets defined by 'start-end,start-end,...'.
    *
    * @param electrostatics Input string
    */
   public void setElectrostatics(String electrostatics) {
     if (electrostatics != null) {
       String[] tokens = electrostatics.split(",");
       Atom[] atoms = molecularAssembly.getAtomArray();
       for (String tok : tokens) {
         Matcher m = atRangePatt.matcher(tok);
         if (m.matches()) {
           int begin = Integer.parseInt(m.group(1));
           int end = Integer.parseInt(m.group(2));
           logger.info(format(" Inactivating electrostatics for atoms %d-%d", begin, end));
           for (int i = begin; i <= end; i++) {
             Atom ai = atoms[i - 1];
             ai.setElectrostatics(false);
             ai.print(Level.FINE);
           }
         } else {
           logger.info(format(" Discarding electrostatics input %s", tok));
         }
       }
     }
   }
 
   /**
    * Inactivates atom sets defined by 'start-end,start-end,...'.
    *
    * @param iatoms Input string
    */
   public void setInactiveAtoms(String iatoms) {
     if (iatoms != null) {
       String[] tokens = iatoms.split(",");
       Atom[] atoms = molecularAssembly.getAtomArray();
       for (String tok : tokens) {
         Matcher m = atRangePatt.matcher(tok);
         if (m.matches()) {
           int begin = Integer.parseInt(m.group(1));
           int end = Integer.parseInt(m.group(2));
           logger.info(format(" Inactivating atoms %d-%d", begin, end));
           for (int i = begin; i <= end; i++) {
             Atom ai = atoms[i - 1];
             ai.setUse(false);
             ai.print(Level.FINE);
           }
         } else {
           logger.info(format(" Discarding inactive atoms input %s", tok));
         }
       }
     }
   }
 
   /**
    * Sets the angle to change torsions by.
    *
    * @param incr a double.
    */
   public void setIncrement(double incr) {
     this.incr = incr;
   }
 
   /**
    * Sets algorithm to log all torsions/energies (not just to file).
    *
    * @param print a boolean.
    */
   public void setPrint(boolean print) {
     this.print = print;
   }
 
   /**
    * Sets the width around each torsion to search (+/-, so 10 degree width will search a 20 degree
    * arc).
    *
    * @param width a double.
    */
   public void setSearchWidth(double width) {
     this.width = width;
   }
 
   /**
    * Null file indicates to not write a video.
    *
    * @param videoFile Filename for video or null
    */
   public void setVideo(String videoFile) {
     if (videoFile != null) {
       File vidFile = new File(videoFile);
       if (vidFile.exists()) {
         for (int i = 0; i < 1000; i++) {
           vidFile = new File(format("%s_%d", videoFile, i));
           if (!vidFile.exists()) {
             this.videoFile = vidFile;
             writeVideo = true;
             videoFilter = new PDBFilter(this.videoFile, molecularAssembly,
                 molecularAssembly.getForceField(), null);
             videoFilter.setLogWrites(false);
             break;
           }
         }
         if (vidFile.exists()) {
           logger.warning(format(" Could not version video file %s", videoFile));
         }
       } else {
         this.videoFile = vidFile;
         writeVideo = true;
         videoFilter = new PDBFilter(this.videoFile, molecularAssembly,
             molecularAssembly.getForceField(), null);
         videoFilter.setLogWrites(false);
       }
     } else {
       writeVideo = false;
     }
   }
 
   /** Main driver method; spins torsions, evaluates energy, and prints to file. */
   public void tryRotamers() {
     try (BufferedWriter bw = new BufferedWriter(new FileWriter(outFile))) {
       if (aroundLibrary) {
         for (Rotamer rotamer : baselineRotamers) {
           applyLibRotamer(rotamer);
           turnChi(startDepth, bw);
         }
       } else {
         RotamerLibrary.measureRotamer(residue, currentChi, false);
         turnChi(startDepth, bw);
       }
     } catch (IOException ex) {
       logger.warning(format(" IO exception in rotamer generation: %s", ex));
     }
   }
 
   /**
    * Applies a library rotamer, filling in the end with 0s as necessary. For example, PTR requires
    * more torsions than TYR, so one cannot simply apply a TYR rotamer to a PTR residue.
    *
    * @param rotamer The rotamer to apply.
    */
   private void applyLibRotamer(Rotamer rotamer) {
     double[] rotValues = new double[nChi * 2];
     Arrays.fill(rotValues, 0.0);
     Arrays.fill(currentChi, 0.0);
     int fillTo = Math.min(startDepth, (rotamer.length - 1));
     for (int i = 0; i < fillTo; i++) {
       int ii = 2 * i;
       rotValues[ii] = rotamer.angles[i];
       currentChi[i] = rotamer.angles[i];
       rotValues[ii + 1] = rotamer.sigmas[i];
     }
     Rotamer newRot = generateRotamer(rotValues);
     RotamerLibrary.applyRotamer(residue, newRot);
   }
 
   /**
    * Generates an aa/na/unk Rotamer for the selected residue given values.
    *
    * @param values The values to use.
    * @return The Rotamer.
    */
   private Rotamer generateRotamer(double[] values) {
     switch (residue.getResidueType()) {
       case AA -> {
         AminoAcid3 aa3 = residue.getAminoAcid3();
         return new Rotamer(aa3, values);
       }
       case NA -> {
         NucleicAcid3 na3 = residue.getNucleicAcid3();
         return new Rotamer(na3, values);
       }
       default -> {
         return new Rotamer(values);
       }
     }
   }
 
   /**
    * Recursive method for turning the torsions.
    *
    * @param depth Current depth of the recursion
    * @param bw The BufferedWriter to write to.
    * @throws IOException If there is an IO exception.
    */
   private void turnChi(int depth, BufferedWriter bw) throws IOException {
     double chi = currentChi[depth];
     for (double i = chi - width; i <= chi + width; i += incr) {
       currentChi[depth] = i;
       if (depth == endDepth) {
         evaluateChi(bw);
         if (listener != null) {
           listener.algorithmUpdate(molecularAssembly);
         }
         if (writeVideo) {
           writeSnapshot();
         }
       } else {
         turnChi(depth + 1, bw);
       }
     }
     currentChi[depth] = chi; // Reset the chi value to where it was.
   }
 
   private void writeSnapshot() {
     try (BufferedWriter bw = new BufferedWriter(new FileWriter(videoFile, true))) {
       bw.write(format("MODEL %d", nEval));
       bw.newLine();
       bw.write(format("REMARK 301 TORSIONS %s", formatChi()));
       bw.newLine();
       bw.flush();
       videoFilter.writeFile(videoFile, true);
       bw.write("ENDMDL");
       bw.newLine();
       bw.flush();
     } catch (IOException ex) {
       logger.warning(
           format(" Exception writing to video file %s: " + "%s", videoFile.getName(), ex));
     }
   }
 
   /**
    * Called at a leaf of the recursion.
    *
    * @param bw The BufferedWriter to write to.
    * @throws IOException If there is an IO exception.
    */
   private void evaluateChi(BufferedWriter bw) throws IOException {
     try {
       applyChi();
       double e = currentEnergy();
       String result = format("%s,%12f", formatChi(), e);
       ++nEval;
       if (print) {
         logger.info(format(" Evaluation %10d %s, energy %10.5f kcal/mol", nEval, formatChi(), e));
       }
       bw.write(result);
       bw.newLine();
       if (nEval % 1000 == 0) {
         logger.info(format(" %12.7e states evaluated", (double) nEval));
       }
     } catch (ArithmeticException ex) {
       logger.info(format(" Force field exception at chi %s", formatChi()));
     }
   }
 
   /** Converts the chi array to a Rotamer and applies it. */
   private void applyChi() {
     double[] rotValues = new double[nChi * 2];
     for (int i = 0; i < nChi; i++) {
       int ii = 2 * i;
       rotValues[ii] = currentChi[i];
       rotValues[ii + 1] = 0.0;
     }
     RotamerLibrary.applyRotamer(residue, generateRotamer(rotValues));
   }
 
   /**
    * Returns a formatted String with chi values.
    *
    * @return A formatted String with chi values.
    */
   private String formatChi() {
     StringBuilder sb = new StringBuilder(format("%8f", currentChi[0]));
     for (int i = 1; i < nChi; i++) {
       // sb.append(",").append(currentChi[i]);
       sb.append(format(",%8f", currentChi[i]));
     }
     return sb.toString();
   }
 
   /**
    * Calculates the energy at the current state.
    *
    * @return Energy of the current state.
    */
   private double currentEnergy() throws ArithmeticException {
     if (x == null) {
       int nVar = potential.getNumberOfVariables();
       x = new double[nVar * 3];
     }
     potential.getCoordinates(x);
     return potential.energy(x);
   }
 }