// ******************************************************************************
   //
   // 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.
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  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
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  // ******************************************************************************
  package ffx.crystal;
  
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import javax.annotation.Nullable;
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.Map.Entry;
  import java.util.logging.Logger;
  
  import static ffx.crystal.SymOp.applySymRot;
  import static ffx.crystal.SymOp.applyTransSymRot;
  import static ffx.numerics.math.ScalarMath.mod;
  import static org.apache.commons.math3.util.FastMath.PI;
  import static org.apache.commons.math3.util.FastMath.cos;
  import static org.apache.commons.math3.util.FastMath.floor;
  import static org.apache.commons.math3.util.FastMath.max;
  import static org.apache.commons.math3.util.FastMath.min;
  import static org.apache.commons.math3.util.FastMath.rint;
  
  /**
   * Class to represent a reflection list.
   *
   * @author Timothy D. Fenn
   * @see <a href="http://dx.doi.org/10.1107/S0021889802013420" target="_blank"> Cowtan, K. 2002.
   * Generic representation and evaluation of properties as a function of position in reciprocal
   * space. J. Appl. Cryst. 35:655-663. </a>
   * @since 1.0
   */
  public class ReflectionList {
  
    private static final Logger logger = Logger.getLogger(ReflectionList.class.getName());
  
    /**
     * The HKL list.
     */
    public final ArrayList<HKL> hklList = new ArrayList<>();
    /**
     * The Crystal instance.
     */
    public final Crystal crystal;
    /**
     * The space group.
     */
    public final SpaceGroup spaceGroup;
    /**
     * Resolution instance.
     */
    public final Resolution resolution;
    /**
     * String to HKL look-up.
     */
    final HashMap<String, HKL> hklMap = new HashMap<>();
    /**
     * For binning reflections based on resolution
     */
    public int nBins = 10;
    /**
     * Histogram.
     */
    private final double[] histogram = new double[1001];
    /**
    * Minimum resolution.
    */
   private double minResolution;
   /**
    * Maximum resolution.
    */
   private double maxResolution;
 
   /**
    * Constructor for ReflectionList.
    *
    * @param crystal    a {@link ffx.crystal.Crystal} object.
    * @param resolution a {@link ffx.crystal.Resolution} object.
    */
   public ReflectionList(Crystal crystal, Resolution resolution) {
     this(crystal, resolution, null);
   }
 
   /**
    * Constructor for ReflectionList.
    *
    * @param crystal    a {@link ffx.crystal.Crystal} object.
    * @param resolution a {@link ffx.crystal.Resolution} object.
    * @param properties a {@link org.apache.commons.configuration2.CompositeConfiguration} object.
    */
   public ReflectionList(Crystal crystal, Resolution resolution, CompositeConfiguration properties) {
     this.crystal = crystal;
     this.spaceGroup = crystal.spaceGroup;
     this.resolution = resolution;
 
     int hMax = (int) (this.crystal.a / this.resolution.resolutionLimit());
     int kMax = (int) (this.crystal.b / this.resolution.resolutionLimit());
     int lMax = (int) (this.crystal.c / this.resolution.resolutionLimit());
 
     minResolution = Double.POSITIVE_INFINITY;
     maxResolution = Double.NEGATIVE_INFINITY;
     int n = 0;
 
     HKL hkl = new HKL();
     for (int h = -hMax; h <= hMax; h++) {
       hkl.setH(h);
       for (int k = -kMax; k <= kMax; k++) {
         hkl.setK(k);
         for (int l = -lMax; l <= lMax; l++) {
           hkl.setL(l);
 
           double res = this.crystal.invressq(hkl);
           getEpsilon(hkl);
           LaueSystem laueSystem = spaceGroup.laueSystem;
           if (laueSystem.checkRestrictions(h, k, l)
               && resolution.inInverseResSqRange(res)
               && !hkl.sysAbs()) {
             minResolution = min(res, minResolution);
             maxResolution = max(res, maxResolution);
             String s = (h + "_" + k + "_" + l).intern();
             hklMap.put(s, new HKL(hkl.getH(), hkl.getK(), hkl.getL(), hkl.getEpsilon(), hkl.allowed));
             n++;
           }
         }
       }
     }
 
     n = 0;
     for (Entry<String, HKL> entry : hklMap.entrySet()) {
       HKL ih = entry.getValue();
       ih.setIndex(n);
       hklList.add(ih);
       n++;
     }
 
     // Set up the resolution bins first build a histogram.
     for (HKL ih : hklList) {
       double r = (this.crystal.invressq(ih) - minResolution) / (maxResolution - minResolution);
       int i = (int) (min(r, 0.999) * 1000.0);
       histogram[i + 1] += 1.0;
     }
 
     // Convert to cumulative histogram
     for (int i = 1; i < histogram.length; i++) {
       histogram[i] += histogram[i - 1];
     }
     for (int i = 0; i < histogram.length; i++) {
       histogram[i] /= histogram[histogram.length - 1];
     }
 
     // Assign each reflection to a bin in the range (0-nbins)
     setResolutionBins(properties);
   }
 
   /**
    * Constructor for ReflectionList.
    *
    * @param a          a double.
    * @param b          a double.
    * @param c          a double.
    * @param alpha      a double.
    * @param beta       a double.
    * @param gamma      a double.
    * @param sg         a {@link java.lang.String} object.
    * @param resolution a double.
    */
   public ReflectionList(double a, double b, double c, double alpha, double beta, double gamma,
                         String sg, double resolution) {
     this(new Crystal(a, b, c, alpha, beta, gamma, sg), new Resolution(resolution));
   }
 
   /**
    * findSymHKL
    *
    * @param hkl  a {@link ffx.crystal.HKL} object.
    * @param mate a {@link ffx.crystal.HKL} object.
    * @return a boolean.
    */
   public boolean findSymHKL(HKL hkl, HKL mate) {
     return findSymHKL(hkl, mate, false);
   }
 
   /**
    * findSymHKL
    *
    * @param h    an int.
    * @param k    an int.
    * @param l    an int.
    * @param mate a {@link ffx.crystal.HKL} object.
    * @return a boolean.
    */
   public boolean findSymHKL(int h, int k, int l, HKL mate) {
     return findSymHKL(new HKL(h, k, l), mate, false);
   }
 
   /**
    * findSymHKL
    *
    * @param h         an int.
    * @param k         an int.
    * @param l         an int.
    * @param mate      a {@link ffx.crystal.HKL} object.
    * @param transpose a boolean.
    * @return a boolean.
    */
   public boolean findSymHKL(int h, int k, int l, HKL mate, boolean transpose) {
     return findSymHKL(new HKL(h, k, l), mate, transpose);
   }
 
   /**
    * getHKL
    *
    * @param h an int.
    * @param k an int.
    * @param l an int.
    * @return a {@link ffx.crystal.HKL} object.
    */
   public HKL getHKL(int h, int k, int l) {
     String s = (h + "_" + k + "_" + l);
     return hklMap.get(s);
   }
 
   /**
    * getHKL
    *
    * @param hkl a {@link ffx.crystal.HKL} object.
    * @return a {@link ffx.crystal.HKL} object.
    */
   public HKL getHKL(HKL hkl) {
     return getHKL(hkl.getH(), hkl.getK(), hkl.getL());
   }
 
   /**
    * Get the maximum resolution.
    *
    * @return Maximum resolution
    */
   public double getMaxResolution() {
     return maxResolution;
   }
 
   /**
    * Get the minimum resolution.
    *
    * @return Minimum resolution
    */
   public double getMinResolution() {
     return minResolution;
   }
 
   /**
    * hasHKL
    *
    * @param hkl a {@link ffx.crystal.HKL} object.
    * @return a boolean.
    */
   public boolean hasHKL(HKL hkl) {
     return hasHKL(hkl.getH(), hkl.getK(), hkl.getL());
   }
 
   /**
    * ordinal
    *
    * @param s a double.
    * @return a double.
    */
   public final double ordinal(double s) {
     double r = (s - minResolution) / (maxResolution - minResolution);
     r = min(r, 0.999) * 1000.0;
     int i = (int) r;
     r -= floor(r);
     return ((1.0 - r) * histogram[i] + r * histogram[i + 1]);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String toString() {
     return " Reflection list with "
         + this.hklList.size()
         + " reflections, spacegroup "
         + this.spaceGroup.shortName
         + " resolution limit: "
         + resolution.resolutionLimit();
   }
 
   /**
    * findSymHKL
    *
    * @param hkl       a {@link ffx.crystal.HKL} object.
    * @param mate      a {@link ffx.crystal.HKL} object.
    * @param transpose a boolean.
    * @return a boolean.
    */
   private boolean findSymHKL(HKL hkl, HKL mate, boolean transpose) {
     int nsym = spaceGroup.numPrimitiveSymEquiv;
 
     for (int i = 0; i < nsym; i++) {
       if (transpose) {
         applyTransSymRot(hkl, mate, spaceGroup.symOps.get(i));
       } else {
         applySymRot(hkl, mate, spaceGroup.symOps.get(i));
       }
 
       LaueSystem laueSystem = spaceGroup.laueSystem;
       if (laueSystem.checkRestrictions(mate.getH(), mate.getK(), mate.getL())) {
         return false;
       }
       if (laueSystem.checkRestrictions(-mate.getH(), -mate.getK(), -mate.getL())) {
         mate.setH(-mate.getH());
         mate.setK(-mate.getK());
         mate.setL(-mate.getL());
         return true;
       }
     }
 
     mate.setH(hkl.getH());
     mate.setK(hkl.getK());
     mate.setL(hkl.getL());
     return false;
   }
 
   /**
    * hasHKL
    *
    * @param h an int.
    * @param k an int.
    * @param l an int.
    * @return a boolean.
    */
   private boolean hasHKL(int h, int k, int l) {
     String s = (h + "_" + k + "_" + l);
     return hklMap.containsKey(s);
   }
 
   private void getEpsilon(HKL hkl) {
     int epsilon = 1;
     int allowed = 255;
 
     int nSym = spaceGroup.symOps.size();
     for (int i = 1; i < nSym; i++) {
       HKL mate = new HKL();
       SymOp symOp = spaceGroup.symOps.get(i);
       applySymRot(hkl, mate, symOp);
       double shift = symOp.symPhaseShift(hkl);
       if (mate.equals(hkl)) {
         if (cos(shift) > 0.999) {
           epsilon++;
         } else {
           allowed = 0;
           epsilon = 0;
           break;
         }
       } else if (mate.equals(hkl.neg())) {
         // centric reflection
         allowed = (int) rint(mod(-0.5 * shift, PI) / (PI / HKL.ndiv));
       }
     }
     if (hkl.getH() == 0 && hkl.getK() == 0 && hkl.getL() == 0) {
       allowed = 0;
     }
 
     hkl.setEpsilon(epsilon);
     hkl.setAllowed(allowed);
   }
 
   private void setResolutionBins(@Nullable CompositeConfiguration properties) {
     if (properties != null) {
       nBins = properties.getInt("reflection-bins", 10);
     }
     double nBinsDouble = nBins;
     for (HKL ih : hklList) {
       int bin = (int) (nBinsDouble * ordinal(crystal.invressq(ih)));
       ih.bin = min(bin, nBins - 1);
     }
   }
 }