// ******************************************************************************
   //
   // 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.cli;
  
  import static java.lang.Integer.parseInt;
  
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.algorithms.optimize.RotamerOptimization.Algorithm;
  import ffx.numerics.math.DoubleMath;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.*;
  
  import java.io.File;
  import java.util.*;
  import java.util.logging.Logger;
  
  import picocli.CommandLine.ArgGroup;
  import picocli.CommandLine.Option;
  
  /**
   * Represents command line options for scripts that use a many-body expansion for global
   * optimization.
   *
   * @author Michael J. Schnieders
   * @author Mallory R. Tollefson
   * @since 1.0
   */
  public class ManyBodyOptions {
  
    private static final Logger logger = Logger.getLogger(ManyBodyOptions.class.getName());
  
    /**
     * The ArgGroup keeps the ManyBodyOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Many-Body Optimization Options%n", validate = false)
    private final ManyBodyOptionGroup group = new ManyBodyOptionGroup();
  
    /**
     * The ArgGroup keeps the BoxOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Many-Body Box Optimization Options%n", validate = false)
    private final BoxOptionGroup boxGroup = new BoxOptionGroup();
  
    /**
     * The ArgGroup keeps the WindowOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Many-Body Window Optimization Options%n", validate = false)
    private final WindowOptionGroup windowGroup = new WindowOptionGroup();
  
    /**
     * The ArgGroup keeps the WindowOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Many-Body Energy Expansion and Cut-off Options%n", validate = false)
    private final EnergyOptionGroup energyGroup = new EnergyOptionGroup();
  
    /**
     * The ArgGroup keeps the ResidueOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Many-Body Residue Selection Options%n", validate = false)
    private final ResidueOptionGroup residueGroup = new ResidueOptionGroup();
  
    private RotamerOptimization rotamerOptimization;
    private RotamerLibrary rotamerLibrary;
  
   /**
    * initRotamerOptimization.
    *
    * @param rotamerOptimization a {@link RotamerOptimization} object.
    * @param activeAssembly a {@link ffx.potential.MolecularAssembly} object.
    */
   public void initRotamerOptimization(RotamerOptimization rotamerOptimization,
       MolecularAssembly activeAssembly) {
     this.rotamerOptimization = rotamerOptimization;
 
     // Collect the residues to optimize.
     List<Residue> residues = collectResidues(activeAssembly);
     rotamerOptimization.setResidues(residues);
     rotamerOptimization.setRotamerLibrary(rotamerLibrary);
 
     // If the user has not selected an algorithm, it will be chosen based on the number of residues.
     Algorithm algorithm = getAlgorithm(residues.size());
 
     // Configure general options.
     rotamerOptimization.setDecomposeOriginal(group.decompose);
     rotamerOptimization.setUseGoldstein(!group.dee);
     rotamerOptimization.setRevert(group.revert);
     boolean monteCarloBool = group.monteCarlo > 1;
     rotamerOptimization.setMonteCarlo(monteCarloBool, group.monteCarlo);
     File energyRestartFile;
     if (!group.energyRestart.equalsIgnoreCase("none")) {
       energyRestartFile = new File(group.energyRestart);
       rotamerOptimization.setEnergyRestartFile(energyRestartFile);
     }
 
     // Configure Energy Expansion and Pruning Options.
     rotamerOptimization.setTwoBodyCutoff(energyGroup.twoBodyCutoff);
     rotamerOptimization.setThreeBodyEnergy(energyGroup.threeBody);
     rotamerOptimization.setThreeBodyCutoff(energyGroup.threeBodyCutoff);
     rotamerOptimization.setDistanceCutoff(energyGroup.cutoff);
     rotamerOptimization.setPruning(energyGroup.prune);
     rotamerOptimization.setSingletonClashThreshold(energyGroup.clashThreshold);
     rotamerOptimization.setPairClashThreshold(energyGroup.pairClashThreshold);
 
     // Window
     if (algorithm == Algorithm.WINDOW) {
       rotamerOptimization.setWindowSize(windowGroup.window);
       rotamerOptimization.setIncrement(windowGroup.increment);
     } else if (algorithm == Algorithm.BOX) {
       // Box
       parseBoxSelection();
       if (boxGroup.approxBoxLength < 0) {
         logger.info(" Negative box length value changed to -1 * input.");
         boxGroup.approxBoxLength *= -1;
       }
       rotamerOptimization.setBoxBorderSize(boxGroup.boxBorderSize);
       rotamerOptimization.setApproxBoxLength(boxGroup.approxBoxLength);
       rotamerOptimization.setNumXYZBoxes(boxGroup.numXYZBoxes);
       rotamerOptimization.setBoxInclusionCriterion(boxGroup.boxInclusionCriterion);
       rotamerOptimization.setBoxStart(boxGroup.initialBox);
       rotamerOptimization.setBoxEnd(boxGroup.finalBox);
       rotamerOptimization.setTitrationBoxes(boxGroup.boxTitration);
       rotamerOptimization.setTitrationBoxSize(boxGroup.approxBoxLength);
     }
   }
 
   /**
    * Collect residues based on residue selection flags.
    *
    * @param activeAssembly a {@link ffx.potential.MolecularAssembly} object.
    */
   public List<Residue> collectResidues(MolecularAssembly activeAssembly) {
 
     // Force re-initialization RotamerLibrary prior to collecting residues and rotamers.
     initRotamerLibrary(true);
 
     // First, interpret the residueGroup.listResidues flag if its set.
     if (!residueGroup.listResidues.isEmpty() && !residueGroup.listResidues.equalsIgnoreCase("none")) {
       List<String> stringList = new ArrayList<>();
       String[] tok = residueGroup.listResidues.split(",");
       Collections.addAll(stringList, tok);
       List<Residue> residueList = new ArrayList<>();
       Polymer[] polymers = activeAssembly.getChains();
       for (String s : stringList) {
         Character chainID = s.charAt(0);
         int i = parseInt(s.substring(1));
         for (Polymer polymer : polymers) {
           if (polymer.getChainID() == chainID) {
             List<Residue> residues = polymer.getResidues();
             for (Residue residue : residues) {
               if (residue.getResidueNumber() == i) {
                 Rotamer[] rotamers = residue.setRotamers(rotamerLibrary);
                 if (rotamers != null && rotamers.length > 0) {
                   residueList.add(residue);
                 }
               }
             }
           }
         }
       }
       return residueList;
     }
 
     // Check that the finish flag is greater than the start flag.
     if (residueGroup.finish < residueGroup.start) {
       residueGroup.finish = Integer.MAX_VALUE;
     }
     Character chainID = null;
     if (!residueGroup.chain.equalsIgnoreCase("-1")) {
       chainID = residueGroup.chain.charAt(0);
     }
 
     // Otherwise, collect all residues with a rotamer.
     List<Residue> residueList = new ArrayList<>();
     Polymer[] polymers = activeAssembly.getChains();
     for (Polymer polymer : polymers) {
       // Enforce requested chainID.
       if (chainID != null && chainID != polymer.getChainID()) {
         continue;
       }
       List<Residue> residues = polymer.getResidues();
       for (Residue residue : residues) {
         int resID = residue.getResidueNumber();
         // Enforce requested residue range.
         if (resID >= residueGroup.start && resID <= residueGroup.finish) {
           Rotamer[] rotamers = residue.setRotamers(rotamerLibrary);
           if (rotamers != null) {
             residueList.add(residue);
           }
         }
       }
     }
 
     return residueList;
   }
 
   /**
    * Returns the user selected algorithm or one chosen based on number of residues.
    *
    * @return Returns the algorithm choice.
    */
   public Algorithm getAlgorithm(int numResidues) {
     if (group.algorithm == 0) {
       if (numResidues < 100) {
         return Algorithm.ALL;
       } else {
         return Algorithm.BOX;
       }
     }
     return Algorithm.getAlgorithm(group.algorithm);
   }
 
   public boolean getUsingOriginalCoordinates() {
     return !group.noOriginal;
   }
 
   public void setOriginalCoordinates(boolean useOrig) {
     group.noOriginal = !useOrig;
   }
 
   public double getApproximate() {
     return rotamerOptimization.getApproximate();
   }
 
   /**
    * Gets the restart file created during rotamer optimization.
    *
    * @return The restart file.
    */
   public File getRestartFile() {
     return rotamerOptimization.getRestartFile();
   }
 
   public RotamerLibrary getRotamerLibrary(boolean reinit) {
     initRotamerLibrary(reinit);
     return rotamerLibrary;
   }
 
   private void initRotamerLibrary(boolean reinit) {
     if (rotamerLibrary == null || reinit) {
       boolean useOrigCoordsRotamer = !group.noOriginal;
       if (group.decompose) {
         useOrigCoordsRotamer = true;
       }
       rotamerLibrary = new RotamerLibrary(
           RotamerLibrary.ProteinLibrary.intToProteinLibrary(group.library), useOrigCoordsRotamer);
     }
   }
 
 
   /** Set allStartResID, boxStart and boxEnd */
   private void parseBoxSelection() {
     // Parse the numBoxes flag.
     String input = boxGroup.numBoxes;
     Scanner boxNumInput = new java.util.Scanner(input);
     boxNumInput.useDelimiter(",");
     int inputLoopCounter = 0;
     int[] numXYZBoxes = new int[3];
     numXYZBoxes[0] = 3; // Default
     while (inputLoopCounter < 3) {
       if (boxNumInput.hasNextInt()) {
         numXYZBoxes[inputLoopCounter] = boxNumInput.nextInt();
         inputLoopCounter++;
       } else if (boxNumInput.hasNextDouble()) {
         numXYZBoxes[inputLoopCounter] = (int) Math.floor(boxNumInput.nextDouble());
         inputLoopCounter++;
         logger.info(" Double input to nB truncated to integer.");
       } else if (boxNumInput.hasNext()) {
         logger.info(" Non-numeric input to nB discarded");
         boxNumInput.next();
       } else {
         logger.info(
             " Insufficient input to nB. Non-input values assumed either equal to X or default to 3");
         break;
       }
     }
     boxNumInput.close();
 
     // Initialize dimensions not provided.
     for (int i = inputLoopCounter; i < 3; i++) {
       numXYZBoxes[i] = numXYZBoxes[0];
     }
 
     // Correct input errors.
     int totalCount = 1;
     for (int i = 0; i < 3; i++) {
       if (numXYZBoxes[i] == 0) {
         numXYZBoxes[i] = 3;
         logger.info(" Input of 0 to nB reset to default of 3.");
       } else if (numXYZBoxes[i] < 0) {
         numXYZBoxes[i] = -1 * numXYZBoxes[i];
         logger.info(" Input of negative number to nB reset to positive number");
       }
       totalCount *= numXYZBoxes[i];
     }
 
     boxGroup.numXYZBoxes = numXYZBoxes;
 
     if (boxGroup.initialBox < 0) {
       boxGroup.initialBox = 0;
     }
     if (boxGroup.finalBox < 0 || boxGroup.finalBox > totalCount) {
       boxGroup.finalBox = totalCount;
     }
 
   }
 
   /** Sets the standard values for properties in rotamer optimization. */
   private void setRotOptProperties(Algorithm algorithm) {
 
   }
 
   public void setAlgorithm(int algorithm) {
     group.algorithm = algorithm;
   }
 
   /**
    * Ponder and Richards (1) or Richardson (2) rotamer library.
    *
    * @return Returns the Rotamer library.
    */
   public int getLibrary() {
     return group.library;
   }
 
   public void setLibrary(int library) {
     group.library = library;
   }
 
   /**
    * Nucleic acid library: currently only Richardson available.
    *
    * @return Returns a String for the nucleic acid library.
    */
   public String getNaLibraryName() {
     return group.naLibraryName;
   }
 
   public void setNaLibraryName(String naLibraryName) {
     group.naLibraryName = naLibraryName;
   }
 
   /**
    * Use dead-end elimination criteria instead of Goldstein criteria.
    *
    * @return Returns true if using DEE instead of Goldstein.
    */
   public boolean isDee() {
     return group.dee;
   }
 
   public void setDee(boolean dee) {
     group.dee = dee;
   }
 
   /**
    * Single character chain ID of the residues to optimize.
    *
    * @return Returns the Chain name.
    */
   public String getChain() {
     return residueGroup.chain;
   }
 
   public void setChain(String chain) {
     residueGroup.chain = chain;
   }
 
   public boolean getOnlyTitration() {
     return residueGroup.onlyTitration;
   }
 
   public void setOnlyTitration(boolean onlyTitration) {
     residueGroup.onlyTitration = onlyTitration;
   }
 
   public int getInterestedResidue() {
     return residueGroup.interestedResidue;
   }
 
   public void setInterestedResidue(int interestedResidue) {
     residueGroup.interestedResidue = interestedResidue;
   }
 
   public double getInclusionCutoff() {
     return residueGroup.inclusionCutoff;
   }
 
   public void setInclusionCutoff(double inclusionCutoff) {
     residueGroup.inclusionCutoff = inclusionCutoff;
   }
 
   /**
    * Starting residue to perform the optimization on (-1 exits). For box optimization, first box to
    * optimize.
    *
    * @return Returns the starting index.
    */
   public int getStart() {
     return residueGroup.start;
   }
 
   public void setStart(int start) {
     residueGroup.start = start;
   }
 
   /**
    * Final residue to perform the optimization on (-1 exits). For box optimization, final box to
    * optimize.
    *
    * @return Returns the finish index.
    */
   public int getFinish() {
     return residueGroup.finish;
   }
 
   public void setFinish(int finish) {
     residueGroup.finish = finish;
   }
 
   /**
    * Cutoff distance for two-body interactions.
    *
    * @return Returns the 2-body cutoff.
    */
   public double getTwoBodyCutoff() {
     return energyGroup.twoBodyCutoff;
   }
 
   public void setTwoBodyCutoff(double twoBodyCutoff) {
     energyGroup.twoBodyCutoff = twoBodyCutoff;
   }
 
   /**
    * -T or --threeBody Include 3-Body interactions in the elimination criteria.
    *
    * @return Returns true if 3-body interactions are being used.
    */
   public boolean isThreeBody() {
     return energyGroup.threeBody;
   }
 
   public void setThreeBody(boolean threeBody) {
     energyGroup.threeBody = threeBody;
   }
 
   /**
    * Cutoff distance for three-body interactions.
    *
    * @return Returns the 3-body cutoff.
    */
   public double getThreeBodyCutoff() {
     return energyGroup.threeBodyCutoff;
   }
 
   public void setThreeBodyCutoff(double threeBodyCutoff) {
     energyGroup.threeBodyCutoff = threeBodyCutoff;
   }
 
   /**
    * Prune no clashes (0), only single clashes (1), or all clashes (2).
    *
    * @return Returns the pruning condition.
    */
   public int getPrune() {
     return energyGroup.prune;
   }
 
   public void setPrune(int prune) {
     energyGroup.prune = prune;
   }
 
   /**
    * Revert unfavorable changes.
    *
    * @return Returns true if unfavorable changes are reverted.
    */
   public boolean isRevert() {
     return group.revert;
   }
 
   public void setRevert(boolean revert) {
     group.revert = revert;
   }
 
   /**
    * Energy restart file from a previous run (requires that all parameters are the same).
    *
    * @return Returns the energy restart file to use.
    */
   public String getEnergyRestart() {
     return group.energyRestart;
   }
 
   public void setEnergyRestart(String energyRestart) {
     group.energyRestart = energyRestart;
   }
 
   /**
    * Do not include starting coordinates as their own rotamer.
    *
    * @return Returns true if original side-chain coordinates should not be used as a rotamer.
    */
   public boolean isNoOriginal() {
     return group.noOriginal;
   }
 
   public void setNoOriginal(boolean noOriginal) {
     group.noOriginal = noOriginal;
   }
 
   /**
    * -E or --decompose Print energy decomposition for the input structure (no optimization).
    *
    * @return Returns true if the input structure should undergo an energy decomposition.
    */
   public boolean isDecompose() {
     return group.decompose;
   }
 
   public void setDecompose(boolean decompose) {
     group.decompose = decompose;
   }
 
   /**
    * Choose a list of individual residues to optimize (eg. A11,A24,B40).
    *
    * @return Returns the list of selected residues.
    */
   public String getListResidues() {
     return residueGroup.listResidues;
   }
 
   public void setListResidues(String listResidues) {
     residueGroup.listResidues = listResidues;
   }
 
   /**
    * Follow elimination criteria with 'n' Monte Carlo steps, or enumerate all remaining
    * conformations, whichever is smaller.
    *
    * @return Returns the number of Monte Carlo optimization steps to apply.
    */
   public int getMonteCarlo() {
     return group.monteCarlo;
   }
 
   public void setMonteCarlo(int monteCarlo) {
     group.monteCarlo = monteCarlo;
   }
 
   /**
    * Save eliminated singles and eliminated pairs to a text file (global and box optimization).
    *
    * @return Returns true to Save eliminated rotamers to a file.
    */
   public boolean isSaveOutput() {
     return group.saveOutput;
   }
 
   public void setSaveOutput(boolean saveOutput) {
     group.saveOutput = saveOutput;
   }
 
   /**
    * Size of the sliding window with respect to adjacent residues (default = 7).
    *
    * @return Returns the sliding window size.
    */
   public int getWindow() {
     return windowGroup.window;
   }
 
   public void setWindow(int window) {
     windowGroup.window = window;
   }
 
   /**
    * Sliding window increment (default = 3).
    *
    * @return Returns the sliding window increment.
    */
   public int getIncrement() {
     return windowGroup.increment;
   }
 
   public void setIncrement(int increment) {
     windowGroup.increment = increment;
   }
 
   /**
    * The sliding window and box cutoff radius (Angstroms).
    *
    * @return Returns the sliding window cutoff radius.
    */
   public double getCutoff() {
     return energyGroup.cutoff;
   }
 
   public void setCutoff(double cutoff) {
     energyGroup.cutoff = cutoff;
   }
 
   /**
    * The threshold for pruning clashes. If two self-energies on the same residue have an energy
    * difference greater than 25 kcal/mol, the high energy rotamers get pruned.
    *
    * @return Returns the clash threshold for self energies.
    */
   public double getClashThreshold() {
     return energyGroup.clashThreshold;
   }
 
   public void setClashThreshold(double clashThreshold) {
     energyGroup.clashThreshold = clashThreshold;
   }
 
   /**
    * The threshold for pruning clashes. If two pair-energies on the same residues have an energy
    * difference greater than 25 kcal/mol, the high energy rotamers get pruned.
    *
    * @return Returns the clash threshold for pair energies.
    */
   public double getPairClashThreshold() {
     return energyGroup.pairClashThreshold;
   }
 
   public void setPairClashThreshold(double pairClashThreshold) {
     energyGroup.pairClashThreshold = pairClashThreshold;
   }
 
   /**
    * The number of boxes along X, Y, and Z (default: '3,3,3').
    *
    * @return Returns the number of boxes.
    */
   public String getNumBoxes() {
     return boxGroup.numBoxes;
   }
 
   public void setNumBoxes(String numBoxes) {
     boxGroup.numBoxes = numBoxes;
   }
 
   /**
    * Extent of overlap between optimization boxes (default: 0.0 A).
    *
    * @return Returns the overlap between optimization boxes.
    */
   public double getBoxBorderSize() {
     return boxGroup.boxBorderSize;
   }
 
   public void setBoxBorderSize(double boxBorderSize) {
     boxGroup.boxBorderSize = boxBorderSize;
   }
 
   /**
    * Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes). Box sizes are
    * rounded up to make a whole number of boxes along each axis (default of 0 disables this
    * function).
    *
    * @return Returns the approximate box length.
    */
   public double getApproxBoxLength() {
     return boxGroup.approxBoxLength;
   }
 
   public void setApproxBoxLength(double approxBoxLength) {
     boxGroup.approxBoxLength = approxBoxLength;
   }
 
   /**
    * Criterion to use for adding residues to boxes. (1) uses C alpha only (N1/9 for nucleic acids)
    * (2) uses any atom. (3) uses any rotamer.
    *
    * @return Returns the Box inclusion criteria.
    */
   public int getBoxInclusionCriterion() {
     return boxGroup.boxInclusionCriterion;
   }
 
   public void setBoxInclusionCriterion(int boxInclusionCriterion) {
     boxGroup.boxInclusionCriterion = boxInclusionCriterion;
   }
 
   public void setBoxTitration(boolean boxTitration){boxGroup.boxTitration = boxTitration;}
 
   public boolean getBoxTitration(){return boxGroup.boxTitration;}
 
   public void setTitrationPH(double pH) {
     group.titrationPH = pH;
   }
 
   public double getTitrationPH() {
     return group.titrationPH;
   }
 
   public void setPHRestraint(double pHRestraint) {
     energyGroup.pHRestraint = pHRestraint;
   }
 
   public double getPHRestraint() {
     return energyGroup.pHRestraint;
   }
 
   public boolean isTitrating() {
     return group.titrationPH == 0;
   }
 
   public boolean getTitration() {
     return group.titration;
   }
 
   public String selectInclusionResidues(final List<Residue> residueList, int mutatingResidue, boolean onlyTitration,
                                        double inclusionCutoff){
     String listResidues = "";
     if (mutatingResidue != -1 && inclusionCutoff != -1) {
       List<Integer> residueNumber = new ArrayList<>();
       for (Residue residue : residueList) {
         residueNumber.add(residue.getResidueNumber());
       }
       double[] mutatingResCoor = new double[3];
       int index = residueNumber.indexOf(mutatingResidue);
       mutatingResCoor = residueList.get(index).getAtomByName("CA", true).getXYZ(mutatingResCoor);
       for (Residue residue: residueList) {
         double[] currentResCoor = new double[3];
         currentResCoor = residue.getAtomByName("CA", true).getXYZ(currentResCoor);
         double dist = DoubleMath.dist(mutatingResCoor, currentResCoor);
         if (dist < inclusionCutoff) {
           listResidues += "," + residue.getChainID() + residue.getResidueNumber();
         }
       }
       listResidues = listResidues.substring(1);
     } else if (onlyTitration){
       String[] titratableResidues = new String[]{"HIS", "HIE", "HID", "GLU", "GLH", "ASP", "ASH", "LYS", "LYD", "CYS", "CYD"};
       List<String> titratableResiudesList = Arrays.asList(titratableResidues);
       for (Residue residue : residueList) {
         if (titratableResiudesList.contains(residue.getName())) {
           String titrateResNum = Integer.toString(residue.getResidueNumber());
           if(!listResidues.contains(titrateResNum)){
             listResidues += "," + residue.getChainID()+ titrateResNum;
           }
           if (inclusionCutoff != -1){
             for (Residue residue2: residueList) {
               boolean includeResidue = evaluateAllRotDist(residue, residue2, inclusionCutoff);
               if(includeResidue){
                 String residue2Number = Integer.toString(residue2.getResidueNumber());
                 if(!listResidues.contains(residue2Number)){
                   listResidues += "," + residue2.getChainID()+ residue2Number;
                 }
               }
             }
           }
 
         }
 
       }
 
       listResidues = listResidues.substring(1);
     }
     return listResidues;
   }
   private static boolean evaluateAllRotDist(Residue residueA, Residue residueB, double inclusionCutoff){
     residueA.setRotamers(RotamerLibrary.getDefaultLibrary());
     residueB.setRotamers(RotamerLibrary.getDefaultLibrary());
     Rotamer[] rotamersA = residueA.getRotamers();
     Rotamer[] rotamersB = residueB.getRotamers();
     double[] aCoor = new double[3];
     double[] bCoor = new double[3];
     try {
       int a = rotamersA.length;
       int b = rotamersB.length;
     } catch (Exception e){
       return false;
     }
 
     for(Rotamer rotamerA: rotamersA){
       residueA.setRotamer(rotamerA);
       for(Rotamer rotamerB: rotamersB){
         residueB.setRotamer(rotamerB);
         for(Atom atomA: residueA.getAtomList()){
           for(Atom atomB: residueB.getAtomList()){
             double dist = DoubleMath.dist(atomA.getXYZ(aCoor), atomB.getXYZ(bCoor));
             if(dist <= inclusionCutoff){
               return true;
             }
           }
         }
       }
     }
 
     return false;
   }
 
 
   /**
    * Collection of ManyBody Options.
    */
   private static class ManyBodyOptionGroup {
 
     /**
      * -a or --algorithm Choices are independent residues (1), all with rotamer elimination (2), all
      * brute force (3), sliding window (4), or box optimization (5).
      */
     @Option(names = {"-a",
         "--algorithm"}, paramLabel = "0", defaultValue = "0", description = "Algorithm: default automatic settings (0), independent residues (1), all with rotamer elimination (2), all brute force (3), sliding window (4), or box optimization (5)")
     private int algorithm;
 
     /** -L or --library Choose either Ponder and Richards (1) or Richardson (2) rotamer library. */
     @Option(names = {"-L",
         "--library"}, paramLabel = "2", defaultValue = "2", description = "Ponder and Richards (1) or Richardson (2) rotamer library.")
     private int library;
 
     /** -nl or --nucleicLibrary Choose a nucleic acid library: currently only Richardson available. */
     // @Option(
     //    names = {"--nl", "--nucleiclibrary"},
     //    paramLabel = "Richardson",
     //    defaultValue = "Richardson",
     //    description = "Nucleic acid library to select: [Richardson]")
     private String naLibraryName = "Richardson";
 
     /** --dee or --deadEnd Use dead-end elimination criteria instead of Goldstein criteria. */
     @Option(names = {"--dee",
         "--deadEnd"}, paramLabel = "false", defaultValue = "false", description = "Use dead-end elimination criteria instead of Goldstein criteria.")
     private boolean dee;
 
     /** -z or --revert Revert unfavorable changes. */
     @Option(names = {"-z",
         "--revert"}, defaultValue = "true", description = "Revert unfavorable changes.")
     private boolean revert;
 
     /**
      * --eR or --energyRestart Load energy restart file from a previous run (requires that all
      * parameters are the same).
      */
     @Option(names = {"--eR",
         "--energyRestart"}, paramLabel = "none", defaultValue = "none", description = "Load energy restart file from a previous run (requires that all parameters are the same).")
     private String energyRestart;
 
     /** -O or --noOriginal Do not include starting coordinates as their own rotamer. */
     @Option(names = {"-O",
         "--noOriginal"}, defaultValue = "false", description = "Do not include starting coordinates as their own rotamer.")
     private boolean noOriginal;
 
     /** -E or --decompose Print energy decomposition for the input structure (no optimization). */
     @Option(names = {"-E",
         "--decompose"}, defaultValue = "false", description = "Print energy decomposition for the input structure (no optimization!).")
     private boolean decompose;
 
     /**
      * --pH or --titrationPH Optimize the titration state of ASP, GLU, HIS and LYS residues.
      */
     @Option(names = {"--pH",
         "--titrationPH"}, paramLabel = "0", defaultValue = "0", description = " Optimize the titration state of ASP, GLU, HIS and LYS residues at the given pH (pH = 0 turns off titration")
     private double titrationPH;
 
     /**
      * --pH or --titrationPH Optimize the titration state of ASP, GLU, HIS and LYS residues.
      */
     @Option(names = {"--tR",
             "--titration"}, paramLabel = "false", defaultValue = "false", description = " Turn on titration state optimization")
     private boolean titration;
 
     /**
      * --mC or --monteCarlo Follow elimination criteria with 'n' Monte Carlo steps, or enumerate all
      * remaining conformations, whichever is smaller.
      */
     @Option(names = {"--mC",
         "--monteCarlo"}, paramLabel = "-1", defaultValue = "-1", description = "Follow elimination criteria with (n) Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.")
     private int monteCarlo;
 
     /**
      * -out or --output Save eliminated singles and eliminated pairs to a text file (global and box
      * optimization).
      */
     //  @Option(
     //      names = {"--out", "--output"},
     //      defaultValue = "false",
     //      description = "Save eliminated singles and eliminated pairs to a text file.")
     private boolean saveOutput;
 
   }
 
   /**
    * Collection of ManyBody Box Optimization Options.
    */
   private static class BoxOptionGroup {
 
     /** -nB or --numBoxes Specify number of boxes along X, Y, and Z (default: '3,3,3'). */
     @Option(names = {"--nB",
         "--numBoxes"}, paramLabel = "3,3,3", defaultValue = "3,3,3", description = "Specify number of boxes along X, Y, and Z (default: 3,3,3)")
     private String numBoxes;
 
     /**
      * Result of parsing numBoxes flag.
      */
     private int[] numXYZBoxes;
 
     /** -bB or --boxBorderSize Extent of overlap between optimization boxes (default: 0.0 A). */
     @Option(names = {"--bB",
         "--boxBorderSize"}, paramLabel = "0.0", defaultValue = "0.0", description = "Extent of overlap between optimization boxes in Angstroms.")
     private double boxBorderSize;
 
     /**
      * -bL or --approxBoxLength Approximate side lengths of boxes to be constructed (over-rides
      * numXYZBoxes). Box sizes are rounded up to make a whole number of boxes along each axis
      * (default of 0 disables this function).
      */
     @Option(names = {"--bL",
         "--approxBoxLength"}, paramLabel = "20.0", defaultValue = "20.0", description = "Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes).")
     private double approxBoxLength;
 
     /**
      * -bC or --boxInclusionCriterion Criterion to use for adding residues to boxes. (1) uses C alpha
      * only (N1/9 for nucleic acids) (2) uses any atom. (3) uses any rotamer
      */
     @Option(names = {"--bC",
         "--boxInclusionCriterion"}, paramLabel = "1", defaultValue = "1", description = "Criterion to use for adding a residue to a box: (1) uses C alpha only (N1/9 for nucleic acids), (2) uses any atom, and (3) uses any rotamer")
     private int boxInclusionCriterion;
 
     /**
      * --iB or --initialBox Initial box to optimize.
      */
     @Option(names = {"--iB", "--initialBox"}, defaultValue = "0", description = "Initial box to optimize.")
     private int initialBox;
 
     /**
      * --fB or --boxFinal Final box to optimize.
      */
     @Option(names = {"--fB", "--finalBox"}, defaultValue = "2147483647", // Integer.MAX_VALUE
         description = "Final box to optimize.")
     private int finalBox;
 
     /**
      * --bT or --boxTitration Center boxes around titratable residues.
      */
     @Option(names = {"--bT", "--boxTitration"}, defaultValue = "false", // Integer.MAX_VALUE
             description = "Center boxes around titratable residues.")
     private boolean boxTitration;
 
   }
 
   /**
    * Collection of ManyBody Window Optimization Options.
    */
   private static class WindowOptionGroup {
 
     /** --window Size of the sliding window with respect to adjacent residues (default = 7). */
     @Option(names = {
         "--window"}, paramLabel = "7", defaultValue = "7", description = "Size of the sliding window with respect to adjacent residues.")
     private int window;
 
     /** --increment Sliding window increment (default = 3). */
     @Option(names = {
         "--increment"}, paramLabel = "3", defaultValue = "3", description = "Sliding window increment.")
     private int increment;
 
   }
 
   /**
    * Collection of ManyBody Energy Optimization Options.
    */
   private static class EnergyOptionGroup {
 
     /** --radius The sliding window and box cutoff radius (Angstroms). */
     @Option(names = {
         "--radius"}, paramLabel = "2.0", defaultValue = "2.0", description = "The sliding box and window cutoff radius (Angstroms).")
     private double cutoff;
 
     /** --tC or --twoBodyCutoff Cutoff distance for two-body interactions. */
     @Option(names = {"--tC",
         "--twoBodyCutoff"}, paramLabel = "3.0", defaultValue = "3.0", description = "Cutoff distance for two body interactions.")
     private double twoBodyCutoff;
 
     /** -T or --threeBody Include 3-Body interactions in the elimination criteria. */
     @Option(names = {"-T",
         "--threeBody"}, defaultValue = "false", description = "Include 3-Body interactions in the elimination criteria.")
     private boolean threeBody;
 
     /** --thC or --threeBodyCutoff Cutoff distance for three-body interactions. */
     @Option(names = {"--thC",
         "--threeBodyCutoff"}, paramLabel = "3.0", defaultValue = "3.0", description = "Cutoff distance for three-body interactions.")
     private double threeBodyCutoff;
 
     /** --pr or --prune Prune no clashes (0), only single clashes (1), or all clashes (2). */
     @Option(names = {"--pr",
         "--prune"}, paramLabel = "1", defaultValue = "1", description = "Prune no clashes (0), only single clashes (1), or all clashes (2)")
     private int prune;
 
     /**
      * --clashThreshold The threshold for pruning clashes. If two self-energies on the same residue
      * have an energy difference greater than 25 kcal/mol, the high energy rotamers get pruned.
      */
     @Option(names = {
         "--clashThreshold"}, paramLabel = "25.0", defaultValue = "25.0", description = "The threshold for pruning clashes.")
     private double clashThreshold;
 
     /**
      * --pairClashThreshold The threshold for pruning clashes. If two pair-energies on the same
      * residues have an energy difference greater than 25 kcal/mol, the high energy rotamers get
      * pruned.
      */
     @Option(names = {
         "--pairClashThreshold"}, paramLabel = "25.0", defaultValue = "25.0", description = "The threshold for pruning pair clashes.")
     private double pairClashThreshold;
 
     /** --radius The sliding window and box cutoff radius (Angstroms). */
     @Option(names = {
             "--kPH", "--pHRestraint"}, paramLabel = "0.0", defaultValue = "0.0", description = "Only allow titration state to change from" +
             "standard state is self energy exceeds the restraint.")
     private double pHRestraint = 0;
   }
 
   /**
    * Collection of ManyBody Residue Selection Options.
    */
   private static class ResidueOptionGroup {
 
     /** --ch or --chain Single character chain ID of the residues to optimize. */
     @Option(names = {"--ch",
         "--chain"}, paramLabel = "<A>", defaultValue = "-1", description = "Include only specified chain ID (default: all chains).")
     private String chain;
 
     /**
      * --sR or --start Starting residue to perform the optimization on.
      */
     @Option(names = {"--sR", "--start"}, defaultValue = "-2147483648", // Integer.MIN_VALUE
         description = "Starting residue to optimize (default: all residues).")
     private int start;
 
     /**
      * --fi or --final Final residue to perform the optimization.
      */
     @Option(names = {"--fR",
         "--final"}, paramLabel = "<final>", defaultValue = "2147483647", // Integer.MAX_VALUE
         description = "Final residue to optimize (default: all residues).")
     private int finish;
 
     /** --lR or --listResidues Choose a list of individual residues to optimize (eg. A11,A24,B40). */
     @Option(names = {"--lR",
         "--listResidues"}, paramLabel = "<list>", defaultValue = "none", description = "Select a list of residues to optimize (eg. A11,A24,B40).")
     private String listResidues;
 
     /** --oT or --onlyTitrtaion Rotamer optimize only titratable residues. */
     @Option(names = {"--oT",
             "--onlyTitration"}, paramLabel = "", defaultValue = "false", description = "Rotamer optimize only titratable residues.")
     private boolean onlyTitration;
 
     /** --iR or --interestedResidue Optimize rotamers within some distance of a specific residue. */
     @Option(names = {"--iR",
             "--interestedResidue"}, paramLabel = "", defaultValue = "-1", description = "Optimize rotamers within some distance of a specific residue.")
     private int interestedResidue = -1;
 
     /** --iC or --inclusionCutoff Distance which rotamers will be included when using only protons, titratable residues, or interested residue. */
     @Option(names = {"--iC",
             "--inclusionCutoff"}, paramLabel = "", defaultValue = "-1", description = "Distance which rotamers will be included when using only protons, titratable residues, or interested residue.")
     private double inclusionCutoff = -1;
 
   }
 
 }