// ******************************************************************************
   //
   // 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
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  // 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
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  package ffx.algorithms.optimize.manybody;
  
  import edu.rit.pj.ParallelTeam;
  import ffx.algorithms.AlgorithmListener;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.crystal.Crystal;
  import ffx.crystal.SymOp;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.MultiResidue;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.ResidueState;
  import ffx.potential.bonded.Rotamer;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.potential.nonbonded.NeighborList;
  import org.apache.commons.math3.util.CombinatoricsUtils;
  import org.apache.commons.math3.util.FastMath;
  
  import java.util.Arrays;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.lang.String.format;
  import static java.util.Arrays.fill;
  import static org.apache.commons.math3.util.FastMath.min;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * Calculates a residue-residue distance matrix.
   *
   * <p>Residue-residue distance is defined as the shortest atom-atom distance in any possible
   * rotamer-rotamer pair if the residues are neighbors (central atom-central atom distances are within
   * a cutoff). Otherwise, distances are set to a default of Double.MAX_VALUE.
   *
   * <p>The intent of using a neighbor list is to avoid tediously searching rotamer- rotamer pairs
   * when two residues are so far apart we will never need the exact distance. We use the distance
   * matrix for adding residues to the sliding window and determining whether to set 3-body energy to
   * 0.0.
   *
   * <p>If the central atoms are too distant from each other, we can safely assume no atoms will ever
   * be close enough for addition to sliding window or to cause explicit calculation of 3-body energy.
   */
  public class DistanceMatrix {
  
    private static final Logger logger = Logger.getLogger(DistanceMatrix.class.getName());
  
    /**
     * MolecularAssembly to perform rotamer optimization on.
     */
    private final MolecularAssembly molecularAssembly;
    /**
     * AlgorithmListener who should receive updates as the optimization runs.
     */
    private final AlgorithmListener algorithmListener;
    /**
     * An array of all residues being optimized. Note that Box and Window optimizations operate on
     * subsets of this list.
     */
    private final Residue[] allResiduesArray;
   /**
    * A list of all residues being optimized. Note that Box and Window optimizations operate on
    * subsets of this list.
    */
   private final List<Residue> allResiduesList;
   /**
    * Number of residues being optimized.
    */
   private final int numResidues;
   /**
    * Default distance method is to find the shortest distance between residues.
    */
   private final RotamerOptimization.DistanceMethod distanceMethod;
   /**
    * The distance that the distance matrix checks for.
    */
   private final double distance;
   /**
    * Two-Body cutoff distance.
    */
   private final double twoBodyCutoffDist;
   /**
    * Three-body cutoff distance.
    */
   private final double threeBodyCutoffDist;
   /**
    * The minimum distance between atoms of a residue pair, taking into account interactions with
    * symmetry mates.
    */
   private NeighborDistances[][] distanceMatrix;
 
   public DistanceMatrix(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener,
                         Residue[] allResiduesArray, List<Residue> allResiduesList,
                         RotamerOptimization.DistanceMethod distanceMethod, double distance, double twoBodyCutoffDist,
                         double threeBodyCutoffDist) {
     this.molecularAssembly = molecularAssembly;
     this.algorithmListener = algorithmListener;
     this.allResiduesArray = allResiduesArray;
     this.allResiduesList = allResiduesList;
     this.numResidues = allResiduesArray.length;
     this.distanceMethod = distanceMethod;
     this.distance = distance;
     this.twoBodyCutoffDist = twoBodyCutoffDist;
     this.threeBodyCutoffDist = threeBodyCutoffDist;
     distanceMatrix();
   }
 
   /**
    * Returns true if all values (usually distances) are both finite and not set to Double.MAX_VALUE.
    *
    * @param values Values to check.
    * @return If all values are regular, finite values.
    */
   private static boolean areFiniteAndNotMax(double... values) {
     return Arrays.stream(values)
         .allMatch((double val) -> Double.isFinite(val) && val < Double.MAX_VALUE);
   }
 
   /**
    * Gets the raw distance between two rotamers using lazy loading of the distance matrix. Intended
    * uses: helper method for get2BodyDistance, and for checking for superpositions.
    *
    * @param i  A residue index.
    * @param ri A rotamer index for i.
    * @param j  A residue index j!=i.
    * @param rj A rotamer index for j.
    * @return dist(i, ri, j, rj), ignoring distance matrix method used.
    */
   public double checkDistMatrix(int i, int ri, int j, int rj) {
     if (i > j) {
       int temp = i;
       i = j;
       j = temp;
       temp = ri;
       ri = rj;
       rj = temp;
     }
     return distanceMatrix[i][ri].getDistance(j, rj);
   }
 
   /**
    * Checks if the i,ri,j,rj pair exceeds the pair distance thresholds.
    *
    * @param i  A residue index.
    * @param ri A rotamer index for i.
    * @param j  A residue index j!=i.
    * @param rj A rotamer index for j.
    * @return If i,ri,j,rj is greater than the threshold distance.
    */
   public boolean checkPairDistThreshold(int i, int ri, int j, int rj) {
     if (twoBodyCutoffDist <= 0 || !Double.isFinite(twoBodyCutoffDist)) {
       return false;
     }
     return (get2BodyDistance(i, ri, j, rj) > twoBodyCutoffDist);
   }
 
   /**
    * Checks if the i,ri,j,rj,k,rk,l,rl quad exceeds the 3-body threshold, or if any component exceeds
    * the pair/triple distance thresholds.
    *
    * @param i  A residue index.
    * @param ri A rotamer index for i.
    * @param j  A residue index j!=i.
    * @param rj A rotamer index for j.
    * @param k  A residue index k!=i, k!=j.
    * @param rk A rotamer index for k.
    * @param l  A residue index l!=i, l!=j, l!=k.
    * @param rl A rotamer index for l.
    * @return If i,ri,j,rj,k,rk,l,rl is greater than the threshold distances.
    */
   public boolean checkQuadDistThreshold(int i, int ri, int j, int rj, int k, int rk, int l, int rl) {
     if (checkTriDistThreshold(i, ri, j, rj, k, rk) || checkTriDistThreshold(i, ri, j, rj, l, rl)
         || checkTriDistThreshold(i, ri, k, rk, l, rl) || checkTriDistThreshold(j, rj, k, rk, l,
         rl)) {
       return true;
     }
     // Use the 3-body cutoff distance for now.
     if (threeBodyCutoffDist <= 0 || !Double.isFinite(threeBodyCutoffDist)) {
       return false;
     }
     return get4BodyDistance(i, ri, j, rj, k, rk, l, rl) > threeBodyCutoffDist;
   }
 
   /**
    * Checks if the i,ri,j,rj,k,rk triple exceeds the 3-body threshold, or if any component exceeds
    * the pair distance threshold.
    *
    * @param i  A residue index.
    * @param ri A rotamer index for i.
    * @param j  A residue index j!=i.
    * @param rj A rotamer index for j.
    * @param k  A residue index k!=i, k!=j.
    * @param rk A rotamer index for k.
    * @return If i,ri,j,rj,k,rk is greater than the threshold distances.
    */
   public boolean checkTriDistThreshold(int i, int ri, int j, int rj, int k, int rk) {
     if (checkPairDistThreshold(i, ri, j, rj) || checkPairDistThreshold(i, ri, k, rk)
         || checkPairDistThreshold(j, rj, k, rk)) {
       return true;
     }
     if (threeBodyCutoffDist <= 0 || !Double.isFinite(threeBodyCutoffDist)) {
       return false;
     }
     return (get3BodyDistance(i, ri, j, rj, k, rk) > threeBodyCutoffDist);
   }
 
   /**
    * Checks the distance matrix, finding the shortest distance between two residues' rotamers or any
    * rotamers from two residues under any symmetry operator; will evaluate this if distance matrix
    * not already filled. Default is to find the shortest distance between two residues rather than
    * between two rotamers.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @return Shortest distance
    */
   public double get2BodyDistance(int i, int ri, int j, int rj) {
     if (i > j) {
       int temp = i;
       i = j;
       j = temp;
       temp = ri;
       ri = rj;
       rj = temp;
     }
 
     if (distanceMethod == RotamerOptimization.DistanceMethod.ROTAMER) {
       return checkDistMatrix(i, ri, j, rj);
     } else {
       return getResidueDistance(i, ri, j, rj);
     }
   }
 
   /**
    * Returns the RMS separation distance for the closest rotamers of three residues' 2-body
    * distances. Defaults to Double.MAX_VALUE when there are pair distances outside cutoffs.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @param k  Residue k
    * @param rk Rotamer for k
    * @return RMS separation distance
    */
   public double get3BodyResidueDistance(int i, int ri, int j, int rj, int k, int rk) {
     double ij = getResidueDistance(i, ri, j, rj);
     double ik = getResidueDistance(i, ri, k, rk);
     double jk = getResidueDistance(j, rj, k, rk);
     if (areFiniteAndNotMax(ij, ik, jk)) {
       return sqrt((ij * ij + ik * ik + jk * jk) / 3.0);
     } else {
       return Double.MAX_VALUE;
     }
   }
 
   /**
    * Returns the RMS separation distance for the closest rotamers of 6 2-body distances from four
    * residues. Defaults to Double.MAX_VALUE when there are pair distances outside cutoffs.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @param k  Residue k
    * @param rk Rotamer for k
    * @param l  Residue l
    * @param rl Rotamer for l
    * @return RMS separation distance
    */
   public double get4BodyResidueDistance(int i, int ri, int j, int rj, int k, int rk, int l, int rl) {
     double ij = getResidueDistance(i, ri, j, rj);
     double ik = getResidueDistance(i, ri, k, rk);
     double il = getResidueDistance(i, ri, l, rl);
     double jk = getResidueDistance(j, rj, k, rk);
     double jl = getResidueDistance(j, rj, l, rl);
     double kl = getResidueDistance(k, rk, l, rl);
     if (areFiniteAndNotMax(ij, ik, il, jk, jl, kl)) {
       return sqrt((ij * ij + ik * ik + il * il + jk * jk + jl * jl + kl * kl) / 6.0);
     } else {
       return Double.MAX_VALUE;
     }
   }
 
   /**
    * Returns the RMS distance between an arbitrary set of rotamers.
    *
    * @param resRot Residue index-rotamer index pairs.
    * @return RMS distance, or Double.MAX_VALUE if ill-defined.
    */
   public double getRawNBodyDistance(int... resRot) {
     int nRes = resRot.length;
     if (nRes % 2 != 0) {
       throw new IllegalArgumentException(" Must have an even number of arguments; res-rot pairs!");
     }
     nRes /= 2;
     if (nRes < 2) {
       throw new IllegalArgumentException(" Must have >= 4 arguments; at least 2 res-rot pairs!");
     }
     // nCr where n is # of residues, choose pairs.
     int numDists = (int) CombinatoricsUtils.binomialCoefficient(nRes, 2);
     double mult = 1.0 / numDists;
     double totDist2 = 0.0;
 
     for (int i = 0; i < nRes - 1; i++) {
       int i2 = 2 * i;
       for (int j = i + 1; j < nRes; j++) {
         int j2 = 2 * j;
         double rawDist = checkDistMatrix(resRot[i2], resRot[i2 + 1], resRot[j2], resRot[j2 + 1]);
         if (!Double.isFinite(rawDist) || rawDist == Double.MAX_VALUE) {
           return Double.MAX_VALUE;
         }
         totDist2 += (rawDist * mult);
       }
     }
     return FastMath.sqrt(totDist2);
   }
 
   /**
    * Checks the distance matrix, finding the shortest distance between the closest rotamers of two
    * residues.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @return Shortest distance
    */
   public double getResidueDistance(int i, int ri, int j, int rj) {
     if (i > j) {
       int temp = i;
       i = j;
       j = temp;
       temp = ri;
       ri = rj;
       rj = temp;
     }
 
     double minDist = Double.MAX_VALUE;
     final int lenri = distanceMatrix[i].length;
     final int lenrj = allResiduesArray[j].getRotamers().length;
     for (int roti = 0; roti < lenri; roti++) {
       for (int rotj = 0; rotj < lenrj; rotj++) {
         minDist = Math.min(minDist, checkDistMatrix(i, roti, j, rotj));
       }
     }
     return minDist;
   }
 
   /**
    * Calculates the minimum distance between two sets of coordinates in a given symmetry operator.
    *
    * @param resi  Coordinates of i by [atom][xyz]
    * @param resj  Coordinates of j by [atom][xyz]
    * @param symOp Symmetry operator to apply
    * @return Minimum distance
    */
   public double interResidueDistance(double[][] resi, double[][] resj, SymOp symOp) {
     double dist = Double.MAX_VALUE;
     Crystal crystal = molecularAssembly.getCrystal();
     for (double[] xi : resi) {
       for (double[] xj : resj) {
         if (symOp != null) {
           crystal.applySymOp(xj, xj, symOp);
         }
         double r = crystal.image(xi[0] - xj[0], xi[1] - xj[1], xi[2] - xj[2]);
         if (r < dist) {
           dist = r;
         }
       }
     }
     return sqrt(dist);
   }
 
   private void distanceMatrix() {
     distanceMatrix = new NeighborDistances[numResidues - 1][];
     for (int i = 0; i < (numResidues - 1); i++) {
       Residue residuei = allResiduesArray[i];
       int lengthRi;
       try {
         lengthRi = residuei.getRotamers().length;
       } catch (IndexOutOfBoundsException ex) {
         logger.warning(format(" Residue i %s has null rotamers.", residuei.toFormattedString(false, true)));
         continue;
       }
       distanceMatrix[i] = new NeighborDistances[lengthRi];
       for (int ri = 0; ri < lengthRi; ri++) {
         distanceMatrix[i][ri] = new NeighborDistances(i, ri);
       }
     }
 
     ResidueState[] orig = ResidueState.storeAllCoordinates(allResiduesList);
     int nMultiRes = 0;
 
     // Build a list that contains one atom from each Residue: CA from
     // amino acids, C1 from nucleic acids, or the first atom otherwise.
     Atom[] atoms = new Atom[numResidues];
     for (int i = 0; i < numResidues; i++) {
       Residue residuei = allResiduesArray[i];
       atoms[i] = residuei.getReferenceAtom();
       if (residuei instanceof MultiResidue) {
         ++nMultiRes;
       }
     }
 
       /*
        Use of the pre-existing ParallelTeam causes a conflict when
        MultiResidues must re-init the force field. Temporary solution
        for sequence optimization: if > 1 residue optimized, run on only
        one thread.
       */
     ParallelTeam parallelTeam = getParallelTeam(nMultiRes);
     Crystal crystal = molecularAssembly.getCrystal();
     int nSymm = crystal.spaceGroup.getNumberOfSymOps();
     logger.info("\n Computing Residue Distance Matrix");
 
     double nlistCutoff = Math.max(Math.max(distance, twoBodyCutoffDist), threeBodyCutoffDist);
 
     // Two residues whose c-alphas are separated by 25 angstroms may
     // still interact if they have long side-chains directed at each other.
     double conservativeBuffer = 25.0;
     nlistCutoff += conservativeBuffer;
 
       /*
        For small crystals, including replicate unit cells in the
        distance matrix is redundant. The cutoff is reduced to the
        interfacial radius.
       */
     if (!crystal.aperiodic()) {
       double sphere = min(min(crystal.interfacialRadiusA, crystal.interfacialRadiusB), crystal.interfacialRadiusC);
       if (nlistCutoff > sphere) {
         nlistCutoff = sphere;
       }
     }
 
     NeighborList neighborList = new NeighborList(null, crystal, atoms, nlistCutoff, 0.0, parallelTeam);
 
     // Expand coordinates
     double[][] xyz = new double[nSymm][3 * numResidues];
     double[] in = new double[3];
     double[] out = new double[3];
     for (int iSymOp = 0; iSymOp < nSymm; iSymOp++) {
       SymOp symOp = crystal.spaceGroup.getSymOp(iSymOp);
       for (int i = 0; i < numResidues; i++) {
         Atom atom = atoms[i];
         in[0] = atom.getX();
         in[1] = atom.getY();
         in[2] = atom.getZ();
         crystal.applySymOp(in, out, symOp);
         int iX = i * 3;
         int iY = iX + 1;
         int iZ = iX + 2;
         xyz[iSymOp][iX] = out[0];
         xyz[iSymOp][iY] = out[1];
         xyz[iSymOp][iZ] = out[2];
       }
     }
 
     // Build the residue neighbor-list.
     int[][][] lists = new int[nSymm][numResidues][];
     boolean[] use = new boolean[numResidues];
     fill(use, true);
     boolean forceRebuild = true;
     boolean printLists = false;
     long neighborTime = -System.nanoTime();
     neighborList.buildList(xyz, lists, use, forceRebuild, printLists);
 
     neighborTime += System.nanoTime();
     logger.info(format(" Built residue neighbor list:           %8.3f sec", neighborTime * 1.0e-9));
 
     DistanceRegion distanceRegion = new DistanceRegion(parallelTeam.getThreadCount(), numResidues,
         crystal, lists, neighborList.getPairwiseSchedule());
 
     long parallelTime = -System.nanoTime();
     try {
       distanceRegion.init(this, molecularAssembly, allResiduesArray, algorithmListener, distanceMatrix);
       parallelTeam.execute(distanceRegion);
     } catch (Exception e) {
       String message = " Exception computing residue distance matrix.";
       logger.log(Level.SEVERE, message, e);
     }
     parallelTime += System.nanoTime();
     logger.info(format(" Pairwise distance matrix:              %8.3f sec", parallelTime * 1.0e-9));
 
     ResidueState.revertAllCoordinates(allResiduesList, orig);
     try {
       parallelTeam.shutdown();
     } catch (Exception ex) {
       logger.warning(format(" Exception shutting down parallel team for the distance matrix: %s", ex));
     }
   }
 
   private ParallelTeam getParallelTeam(int nMultiRes) {
     int nThreads;
     if (molecularAssembly.getPotentialEnergy().getParallelTeam() != null) {
       nThreads = (nMultiRes > 1) ? 1
           : molecularAssembly.getPotentialEnergy().getParallelTeam().getThreadCount();
     } else {
       // Suggested: nThreads = (nMultiRes > 1) ? 1 : ParallelTeam.getDefaultThreadCount();
       nThreads = 16;
     }
     ParallelTeam parallelTeam = new ParallelTeam(nThreads);
     return parallelTeam;
   }
 
   /**
    * Returns the RMS separation distance of three 2-body distances. Defaults to Double.MAX_VALUE when
    * there are pair distances outside cutoffs.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @param k  Residue k
    * @param rk Rotamer for k
    * @return RMS separation distance
    */
   private double get3BodyDistance(int i, int ri, int j, int rj, int k, int rk) {
     double ij = get2BodyDistance(i, ri, j, rj);
     double ik = get2BodyDistance(i, ri, k, rk);
     double jk = get2BodyDistance(j, rj, k, rk);
     if (areFiniteAndNotMax(ij, ik, jk)) {
       return sqrt((ij * ij + ik * ik + jk * jk) / 3.0);
     } else {
       return Double.MAX_VALUE;
     }
   }
 
   /**
    * Returns the RMS separation distance of 6 2-body distances. Defaults to Double.MAX_VALUE when
    * there are pair distances outside cutoffs.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @param k  Residue k
    * @param rk Rotamer for k
    * @param l  Residue l
    * @param rl Rotamer for l
    * @return RMS separation distance
    */
   private double get4BodyDistance(int i, int ri, int j, int rj, int k, int rk, int l, int rl) {
     double ij = get2BodyDistance(i, ri, j, rj);
     double ik = get2BodyDistance(i, ri, k, rk);
     double il = get2BodyDistance(i, ri, l, rl);
     double jk = get2BodyDistance(j, rj, k, rk);
     double jl = get2BodyDistance(j, rj, l, rl);
     double kl = get2BodyDistance(k, rk, l, rl);
     if (areFiniteAndNotMax(ij, ik, il, jk, jl, kl)) {
       return sqrt((ij * ij + ik * ik + il * il + jk * jk + jl * jl + kl * kl) / 6.0);
     } else {
       return Double.MAX_VALUE;
     }
   }
 
   /**
    * Evaluate the pairwise distance between two residues' rotamers under any symmetry operator; does
    * "lazy loading" for the distance matrix.
    *
    * @param i  Residue i
    * @param ri Rotamer for i
    * @param j  Residue j
    * @param rj Rotamer for j
    * @return Shortest distance
    */
   private double evaluateDistance(int i, int ri, int j, int rj) {
     Residue resi = allResiduesArray[i];
     Rotamer[] rotamersI = resi.getRotamers();
     Rotamer roti = rotamersI[ri];
     double[][] xi;
     if (roti.equals(resi.getRotamer())) {
       xi = resi.storeCoordinateArray();
     } else {
       ResidueState origI = resi.storeState();
       RotamerLibrary.applyRotamer(resi, roti);
       xi = resi.storeCoordinateArray();
       resi.revertState(origI);
     }
 
     Residue resj = allResiduesArray[j];
     Rotamer[] rotamersJ = resj.getRotamers();
     Rotamer rotj = rotamersJ[rj];
     double[][] xj;
     if (rotj.equals(resj.getRotamer())) {
       xj = resj.storeCoordinateArray();
     } else {
       ResidueState origJ = resj.storeState();
       RotamerLibrary.applyRotamer(resj, rotj);
       xj = resj.storeCoordinateArray();
       resj.revertState(origJ);
     }
 
     Crystal crystal = molecularAssembly.getCrystal();
     int nSymm = crystal.spaceGroup.getNumberOfSymOps();
     double minDist = Double.MAX_VALUE;
     for (int iSymOp = 0; iSymOp < nSymm; iSymOp++) {
       SymOp symOp = crystal.spaceGroup.getSymOp(iSymOp);
       double dist = interResidueDistance(xi, xj, symOp);
       minDist = Math.min(dist, minDist);
     }
     return minDist;
   }
 
   /**
    * Store all neighbors of a residue / rotamer pair.
    */
   public class NeighborDistances {
 
     /**
      * The residue index.
      */
     private final int i;
     /**
      * The rotamer index.
      */
     private final int ri;
 
     /**
      * Map of distances.
      * <p>
      * The key is the index of residue j.
      * The value is an array of distances for each rotamer of residue j.
      */
     private final Map<Integer, double[]> distances = new HashMap<>();
 
     /**
      * Constructor.
      *
      * @param i  The residue index.
      * @param ri The rotamer index.
      */
     public NeighborDistances(int i, int ri) {
       this.i = i;
       this.ri = ri;
     }
 
     /**
      * Store a distance.
      *
      * @param j        The residue index.
      * @param rj       The rotamer index.
      * @param distance The distance.
      */
     public void storeDistance(int j, int rj, double distance) {
       // Synchronize on the distances map to avoid concurrent modification.
       synchronized (distances) {
         if (distances.containsKey(j)) {
           distances.get(j)[rj] = distance;
         } else {
           double[] dists = new double[allResiduesArray[j].getRotamers().length];
           Arrays.fill(dists, -1);
           dists[rj] = distance;
           distances.put(j, dists);
         }
       }
     }
 
     /**
      * Get a distance.
      *
      * @param j  The residue index.
      * @param rj The rotamer index.
      * @return The distance.
      */
     public double getDistance(int j, int rj) {
       if (distances.containsKey(j) && distances.get(j)[rj] >= 0) {
         return distances.get(j)[rj];
       } else {
         double distance = Double.POSITIVE_INFINITY;
         storeDistance(j, rj, distance);
         return distance;
       }
     }
   }
 
 }